PDB Full entry for 5ZCK 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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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