HEADER PROTEIN FIBRIL 18-FEB-18 5ZCK
TITLE STRUCTURE OF THE RIP3 CORE REGION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PEPTIDE FROM RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN
COMPND 3 KINASE 3;
COMPND 4 CHAIN: A;
COMPND 5 SYNONYM: RIP-3 CORE REGION;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 4 ORGANISM_COMMON: HUMAN;
SOURCE 5 ORGANISM_TAXID: 9606
KEYWDS RIP3, CORE REGION, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR J.LI,H.WU
REVDAT 4 22-NOV-23 5ZCK 1 LINK
REVDAT 3 30-MAY-18 5ZCK 1 JRNL
REVDAT 2 23-MAY-18 5ZCK 1 JRNL REMARK
REVDAT 1 18-APR-18 5ZCK 0
JRNL AUTH M.MOMPEAN,W.LI,J.LI,S.LAAGE,A.B.SIEMER,G.BOZKURT,H.WU,
JRNL AUTH 2 A.E.MCDERMOTT
JRNL TITL THE STRUCTURE OF THE NECROSOME RIPK1-RIPK3 CORE, A HUMAN
JRNL TITL 2 HETERO-AMYLOID SIGNALING COMPLEX.
JRNL REF CELL V. 173 1244 2018
JRNL REFN ISSN 1097-4172
JRNL PMID 29681455
JRNL DOI 10.1016/J.CELL.2018.03.032
REMARK 2
REMARK 2 RESOLUTION. 1.27 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.83
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 3 NUMBER OF REFLECTIONS : 776
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.139
REMARK 3 R VALUE (WORKING SET) : 0.137
REMARK 3 FREE R VALUE : 0.153
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.180
REMARK 3 FREE R VALUE TEST SET COUNT : 79
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 1.3200 - 1.2710 0.98 697 79 0.1371 0.1525
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.420
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 7.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.007 27
REMARK 3 ANGLE : 1.024 36
REMARK 3 CHIRALITY : 0.049 5
REMARK 3 PLANARITY : 0.001 5
REMARK 3 DIHEDRAL : 14.092 9
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5ZCK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-FEB-18.
REMARK 100 THE DEPOSITION ID IS D_1300006852.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 08-OCT-15
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRF
REMARK 200 BEAMLINE : BL19U1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.987
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 776
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270
REMARK 200 RESOLUTION RANGE LOW (A) : 14.830
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2
REMARK 200 DATA REDUNDANCY : 20.00
REMARK 200 R MERGE (I) : 0.08500
REMARK 200 R SYM (I) : NULL
REMARK 200 FOR THE DATA SET : 54.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 2ON9
REMARK 200
REMARK 200 REMARK: LONG NEEDLES
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 19.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.52
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE, 0.1 M SODIUM
REMARK 280 CACODYLATE, 20% (V/V) PEG 200, PH 6.5, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 2.40650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.78200
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 8.57550
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 14.78200
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 2.40650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 8.57550
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA A 101 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HOH A 201 O
REMARK 620 2 HOH A 202 O 57.4
REMARK 620 3 HOH A 202 O 120.6 151.6
REMARK 620 N 1 2
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 101
DBREF 5ZCK A 1 4 UNP Q9Y572 RIPK3_HUMAN 458 461
SEQRES 1 A 4 VAL GLN VAL GLY
HET NA A 101 1
HETNAM NA SODIUM ION
FORMUL 2 NA NA 1+
FORMUL 3 HOH *2(H2 O)
LINK NA NA A 101 O HOH A 201 1555 2555 3.16
LINK NA NA A 101 O HOH A 202 1555 1555 2.38
LINK NA NA A 101 O HOH A 202 1555 1455 2.59
SITE 1 AC1 2 VAL A 1 HOH A 202
CRYST1 4.813 17.151 29.564 90.00 90.00 90.00 P 21 21 21 4
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.207771 0.000000 0.000000 0.00000
SCALE2 0.000000 0.058306 0.000000 0.00000
SCALE3 0.000000 0.000000 0.033825 0.00000
ATOM 1 N VAL A 1 2.742 0.132 5.642 1.00 3.99 N
ATOM 2 CA VAL A 1 2.326 0.709 4.366 1.00 2.56 C
ATOM 3 C VAL A 1 2.933 -0.077 3.215 1.00 1.92 C
ATOM 4 O VAL A 1 4.148 -0.295 3.184 1.00 3.19 O
ATOM 5 CB VAL A 1 2.752 2.184 4.228 1.00 3.07 C
ATOM 6 CG1 VAL A 1 2.296 2.743 2.872 1.00 3.77 C
ATOM 7 CG2 VAL A 1 2.212 3.019 5.377 1.00 3.43 C
ATOM 8 N GLN A 2 2.084 -0.494 2.278 1.00 1.70 N
ATOM 9 CA GLN A 2 2.519 -1.155 1.052 1.00 2.36 C
ATOM 10 C GLN A 2 1.919 -0.420 -0.141 1.00 1.55 C
ATOM 11 O GLN A 2 0.699 -0.239 -0.206 1.00 2.33 O
ATOM 12 CB GLN A 2 2.094 -2.625 1.049 1.00 2.10 C
ATOM 13 CG GLN A 2 2.778 -3.435 2.146 1.00 2.52 C
ATOM 14 CD GLN A 2 2.173 -4.806 2.321 1.00 2.31 C
ATOM 15 OE1 GLN A 2 0.950 -4.969 2.245 1.00 3.55 O
ATOM 16 NE2 GLN A 2 3.018 -5.806 2.550 1.00 3.01 N
ATOM 17 N VAL A 3 2.779 0.013 -1.062 1.00 1.93 N
ATOM 18 CA VAL A 3 2.353 0.679 -2.284 1.00 2.29 C
ATOM 19 C VAL A 3 3.007 -0.025 -3.458 1.00 2.06 C
ATOM 20 O VAL A 3 4.232 -0.183 -3.488 1.00 1.80 O
ATOM 21 CB VAL A 3 2.743 2.181 -2.310 1.00 2.61 C
ATOM 22 CG1 VAL A 3 2.311 2.812 -3.652 1.00 3.61 C
ATOM 23 CG2 VAL A 3 2.142 2.934 -1.116 1.00 3.05 C
ATOM 24 N GLY A 4 2.198 -0.455 -4.422 1.00 3.85 N
ATOM 25 CA GLY A 4 2.735 -1.144 -5.585 1.00 5.65 C
ATOM 26 C GLY A 4 1.938 -0.824 -6.827 1.00 7.85 C
ATOM 27 O GLY A 4 0.850 -0.277 -6.711 1.00 11.13 O
ATOM 28 OXT GLY A 4 2.339 -1.084 -7.959 1.00 9.12 O
TER 29 GLY A 4
HETATM 30 NA NA A 101 0.239 -2.656 5.673 1.00 35.01 NA
HETATM 31 O HOH A 201 0.462 2.091 -6.509 1.00 59.75 O
HETATM 32 O HOH A 202 2.538 -3.238 5.849 1.00 32.69 O
CONECT 30 32
CONECT 32 30
MASTER 205 0 1 0 0 0 1 6 31 1 2 1
END