HEADER SIGNALING PROTEIN 25-JUL-18 6AC5 TITLE CRYSTAL STRUCTURE OF RIPK1 DEATH DOMAIN GLCNACYLATED BY EPEC EFFECTOR TITLE 2 NLEB COMPND MOL_ID: 1; COMPND 2 MOLECULE: RECEPTOR-INTERACTING SERINE/THREONINE-PROTEIN KINASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DEATH DOMAIN; COMPND 5 SYNONYM: CELL DEATH PROTEIN RIP,RECEPTOR-INTERACTING PROTEIN 1,RIP-1, COMPND 6 SERINE/THREONINE-PROTEIN KINASE RIP; COMPND 7 EC: 2.7.11.1; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RIPK1, RIP, RIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P KEYWDS APOPTOSIS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.DING,F.SHAO REVDAT 4 22-NOV-23 6AC5 1 HETSYN REVDAT 3 29-JUL-20 6AC5 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE REVDAT 2 26-JUN-19 6AC5 1 JRNL REVDAT 1 01-MAY-19 6AC5 0 JRNL AUTH J.DING,X.PAN,L.DU,Q.YAO,J.XUE,H.YAO,D.C.WANG,S.LI,F.SHAO JRNL TITL STRUCTURAL AND FUNCTIONAL INSIGHTS INTO HOST DEATH DOMAINS JRNL TITL 2 INACTIVATION BY THE BACTERIAL ARGININE GLCNACYLTRANSFERASE JRNL TITL 3 EFFECTOR. JRNL REF MOL.CELL V. 74 922 2019 JRNL REFN ISSN 1097-2765 JRNL PMID 30979585 JRNL DOI 10.1016/J.MOLCEL.2019.03.028 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17021 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 863 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 26.1306 - 2.6359 0.99 2837 145 0.1789 0.2118 REMARK 3 2 2.6359 - 2.0925 1.00 2733 132 0.1649 0.1726 REMARK 3 3 2.0925 - 1.8281 1.00 2695 139 0.1282 0.1892 REMARK 3 4 1.8281 - 1.6609 1.00 2652 128 0.1162 0.1638 REMARK 3 5 1.6609 - 1.5419 1.00 2630 168 0.1096 0.1554 REMARK 3 6 1.5419 - 1.4510 1.00 2611 151 0.1180 0.1888 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.010 830 REMARK 3 ANGLE : 1.057 1121 REMARK 3 CHIRALITY : 0.085 124 REMARK 3 PLANARITY : 0.008 140 REMARK 3 DIHEDRAL : 14.698 317 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 6AC5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1300008505. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97928 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 32.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6ACI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2 M AMMONIUM SULFATE, 100 MM BIS REMARK 280 -TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.57500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.87500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.87500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.36250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.87500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.87500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.78750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.87500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.87500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 44.36250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.87500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.87500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.78750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 29.57500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 561 REMARK 465 THR A 562 REMARK 465 ASN A 563 REMARK 465 PHE A 564 REMARK 465 LYS A 565 REMARK 465 GLU A 566 REMARK 465 GLU A 567 REMARK 465 PRO A 568 REMARK 465 ALA A 569 REMARK 465 ALA A 570 REMARK 465 LYS A 571 REMARK 465 TYR A 572 REMARK 465 GLN A 573 REMARK 465 ASN A 671 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 829 O HOH A 895 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 850 O HOH A 895 3564 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 658 71.79 -115.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6AC0 RELATED DB: PDB DBREF 6AC5 A 561 671 UNP Q13546 RIPK1_HUMAN 561 671 SEQRES 1 A 111 ASN THR ASN PHE LYS GLU GLU PRO ALA ALA LYS TYR GLN SEQRES 2 A 111 ALA ILE PHE ASP ASN THR THR SER LEU THR ASP LYS HIS SEQRES 3 A 111 LEU ASP PRO ILE ARG GLU ASN LEU GLY LYS HIS TRP LYS SEQRES 4 A 111 ASN CYS ALA ARG LYS LEU GLY PHE THR GLN SER GLN ILE SEQRES 5 A 111 ASP GLU ILE ASP HIS ASP TYR GLU ARG ASP GLY LEU LYS SEQRES 6 A 111 GLU LYS VAL TYR GLN MET LEU GLN LYS TRP VAL MET ARG SEQRES 7 A 111 GLU GLY ILE LYS GLY ALA THR VAL GLY LYS LEU ALA GLN SEQRES 8 A 111 ALA LEU HIS GLN CYS SER ARG ILE ASP LEU LEU SER SER SEQRES 9 A 111 LEU ILE TYR VAL SER GLN ASN HET NAG A 701 14 HET SO4 A 702 5 HET SO4 A 703 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG C8 H15 N O6 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *111(H2 O) HELIX 1 AA1 ALA A 574 ASN A 578 5 5 HELIX 2 AA2 THR A 583 LEU A 594 1 12 HELIX 3 AA3 TRP A 598 LEU A 605 1 8 HELIX 4 AA4 THR A 608 TYR A 619 1 12 HELIX 5 AA5 GLY A 623 ALA A 644 1 22 HELIX 6 AA6 THR A 645 CYS A 656 1 12 HELIX 7 AA7 ARG A 658 SER A 669 1 12 SSBOND 1 CYS A 601 CYS A 656 1555 1555 2.04 LINK NH2 ARG A 603 C1 NAG A 701 1555 1555 1.45 CRYST1 55.750 55.750 59.150 90.00 90.00 90.00 P 43 21 2 8 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 0.017937 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017937 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016906 0.00000