HEADER LIGASE/HYDROLASE 06-JAN-20 6LOJ TITLE THE COMPLEX STRUCTURE OF IPAH9.8-LRR AND HGBP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INVASION PLASMID ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LRR DOMAIN; COMPND 5 EC: 6.3.2.-; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GUANYLATE-BINDING PROTEIN 1; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: GTP-BINDING PROTEIN 1,HUGBP-1,GUANINE NUCLEOTIDE-BINDING COMPND 11 PROTEIN 1,INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1; COMPND 12 EC: 3.6.5.-; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SHIGELLA FLEXNERI; SOURCE 3 ORGANISM_TAXID: 623; SOURCE 4 GENE: IPAH9.8, NCTC9783_05321; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: GBP1; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IPAH9.8, HGBP1, LRR, TRANSFERASE, LIGASE-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.YE,H.HUANG REVDAT 3 29-NOV-23 6LOJ 1 REMARK REVDAT 2 30-DEC-20 6LOJ 1 JRNL REVDAT 1 23-DEC-20 6LOJ 0 JRNL AUTH Y.YE,Y.XIONG,H.HUANG JRNL TITL SUBSTRATE-BINDING DESTABILIZES THE HYDROPHOBIC CLUSTER TO JRNL TITL 2 RELIEVE THE AUTOINHIBITION OF BACTERIAL UBIQUITIN LIGASE JRNL TITL 3 IPAH9.8. JRNL REF COMMUN BIOL V. 3 752 2020 JRNL REFN ESSN 2399-3642 JRNL PMID 33303953 JRNL DOI 10.1038/S42003-020-01492-1 REMARK 2 REMARK 2 RESOLUTION. 3.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.590 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 28371 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1416 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 60.9100 - 8.0100 1.00 3002 158 0.2072 0.2181 REMARK 3 2 8.0100 - 6.3600 1.00 2774 146 0.2785 0.3043 REMARK 3 3 6.3600 - 5.5600 1.00 2711 143 0.2669 0.2878 REMARK 3 4 5.5600 - 5.0500 1.00 2693 142 0.2127 0.2594 REMARK 3 5 5.0500 - 4.6900 1.00 2655 140 0.1724 0.2174 REMARK 3 6 4.6900 - 4.4100 1.00 2647 139 0.1805 0.2283 REMARK 3 7 4.4100 - 4.1900 0.99 2646 140 0.2130 0.2750 REMARK 3 8 4.1900 - 4.0100 0.99 2618 135 0.2528 0.2807 REMARK 3 9 4.0100 - 3.8500 1.00 2605 137 0.3052 0.3497 REMARK 3 10 3.8500 - 3.7200 0.99 2605 136 0.3404 0.3644 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 192.1 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -45.3127 28.1399 5.9112 REMARK 3 T TENSOR REMARK 3 T11: 1.7485 T22: 0.8474 REMARK 3 T33: 1.1455 T12: 0.0241 REMARK 3 T13: 0.2423 T23: -0.0121 REMARK 3 L TENSOR REMARK 3 L11: 0.8174 L22: 1.1102 REMARK 3 L33: 2.2120 L12: -0.8232 REMARK 3 L13: -0.7340 L23: 1.3290 REMARK 3 S TENSOR REMARK 3 S11: -0.2669 S12: -0.1897 S13: 0.0902 REMARK 3 S21: 0.3663 S22: 0.4451 S23: 0.0352 REMARK 3 S31: 0.1583 S32: -0.0485 S33: -0.1103 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 6LOJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015159. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28447 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.720 REMARK 200 RESOLUTION RANGE LOW (A) : 60.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 37.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.590 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: 1F5N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.5M NACL, 0.1M K/NA PHOSPHATE BUFFER, REMARK 280 PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 194.11667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 388.23333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 291.17500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 485.29167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 97.05833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 194.11667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 388.23333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 485.29167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 291.17500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 97.05833 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 241 REMARK 465 MET A 242 REMARK 465 SER A 243 REMARK 465 ASP A 244 REMARK 465 MET B -2 REMARK 465 ASP B -1 REMARK 465 PRO B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 159 REMARK 465 GLU B 160 REMARK 465 ASN B 161 REMARK 465 GLU B 162 REMARK 465 ASN B 163 REMARK 465 GLU B 164 REMARK 465 VAL B 165 REMARK 465 GLU B 166 REMARK 465 ASP B 192 REMARK 465 GLY B 193 REMARK 465 GLN B 194 REMARK 465 PRO B 195 REMARK 465 ARG B 586 REMARK 465 LYS B 587 REMARK 465 ALA B 588 REMARK 465 CYS B 589 REMARK 465 THR B 590 REMARK 465 ILE B 591 REMARK 465 SER B 592 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 71 CG CD1 CD2 REMARK 470 LEU A 89 CG CD1 CD2 REMARK 470 ARG A 163 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 MET B 11 CG SD CE REMARK 470 GLU B 15 CG CD OE1 OE2 REMARK 470 TYR B 47 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 TYR B 53 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN B 56 CG OD1 ND2 REMARK 470 LEU B 58 CG CD1 CD2 REMARK 470 LYS B 61 CG CD CE NZ REMARK 470 LYS B 62 CG CD CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 PHE B 65 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU B 67 CG CD1 CD2 REMARK 470 LYS B 76 CG CD CE NZ REMARK 470 GLU B 99 CG CD OE1 OE2 REMARK 470 ASP B 103 CG OD1 OD2 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 ASN B 109 CG OD1 ND2 REMARK 470 ASP B 112 CG OD1 OD2 REMARK 470 ILE B 134 CG1 CG2 CD1 REMARK 470 GLN B 137 CG CD OE1 NE2 REMARK 470 MET B 139 CG SD CE REMARK 470 LEU B 142 CG CD1 CD2 REMARK 470 ARG B 151 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 153 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 155 CG CD CE NZ REMARK 470 PHE B 178 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 183 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 188 CG OD1 OD2 REMARK 470 LEU B 189 CG CD1 CD2 REMARK 470 GLU B 190 CG CD OE1 OE2 REMARK 470 LEU B 196 CG CD1 CD2 REMARK 470 GLU B 200 CG CD OE1 OE2 REMARK 470 LEU B 202 CG CD1 CD2 REMARK 470 TYR B 204 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU B 206 CG CD1 CD2 REMARK 470 LYS B 207 CG CD CE NZ REMARK 470 LYS B 209 CG CD CE NZ REMARK 470 LYS B 210 CG CD CE NZ REMARK 470 GLU B 217 CG CD OE1 OE2 REMARK 470 ILE B 226 CG1 CG2 CD1 REMARK 470 ARG B 240 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 243 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 244 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 246 CG CD CE NZ REMARK 470 GLN B 249 CG CD OE1 NE2 REMARK 470 LEU B 250 CG CD1 CD2 REMARK 470 GLU B 251 CG CD OE1 OE2 REMARK 470 GLN B 254 CG CD OE1 NE2 REMARK 470 ASP B 255 CG OD1 OD2 REMARK 470 GLU B 256 CG CD OE1 OE2 REMARK 470 GLU B 257 CG CD OE1 OE2 REMARK 470 LEU B 258 CG CD1 CD2 REMARK 470 ASP B 259 CG OD1 OD2 REMARK 470 GLU B 261 CG CD OE1 OE2 REMARK 470 ASP B 375 CG OD1 OD2 REMARK 470 LEU B 476 CG CD1 CD2 REMARK 470 GLN B 477 CG CD OE1 NE2 REMARK 470 ASP B 479 CG OD1 OD2 REMARK 470 GLN B 480 CG CD OE1 NE2 REMARK 470 LYS B 487 CG CD CE NZ REMARK 470 LYS B 520 CG CD CE NZ REMARK 470 LEU B 528 CG CD1 CD2 REMARK 470 GLU B 575 CG CD OE1 OE2 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 GLU A 52 NZ LYS B 485 6565 1.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS B 485 CD - CE - NZ ANGL. DEV. = -15.3 DEGREES 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 VAL A 150 -60.62 -106.76 REMARK 500 ALA A 174 94.29 -69.25 REMARK 500 ASN A 179 113.80 -165.41 REMARK 500 PRO A 181 -167.10 -76.90 REMARK 500 PRO A 231 57.68 -69.09 REMARK 500 HIS A 234 59.09 -98.30 REMARK 500 LEU B 46 -166.77 -78.79 REMARK 500 ARG B 48 38.35 39.96 REMARK 500 ASN B 109 0.88 -57.16 REMARK 500 SER B 186 47.21 34.85 REMARK 500 ARG B 240 91.53 61.41 REMARK 500 PRO B 241 154.52 -40.57 REMARK 500 LEU B 247 -161.93 -79.65 REMARK 500 ALA B 248 79.47 -68.05 REMARK 500 ASP B 259 61.41 -152.50 REMARK 500 ASN B 289 -168.62 -125.29 REMARK 500 LYS B 374 60.67 39.70 REMARK 500 ASP B 377 14.77 55.70 REMARK 500 THR B 478 -32.14 -131.80 REMARK 500 GLN B 480 -71.05 -61.93 REMARK 500 THR B 481 -31.31 66.96 REMARK 500 LEU B 482 -167.84 -176.34 REMARK 500 LYS B 485 -26.42 77.04 REMARK 500 GLU B 486 -5.38 -146.90 REMARK 500 GLU B 490 47.52 -88.69 REMARK 500 VAL B 491 -18.15 -141.73 REMARK 500 GLU B 563 50.39 -92.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 601 DBREF1 6LOJ A 22 244 UNP A0A380D7J9_SHIFL DBREF2 6LOJ A A0A380D7J9 22 244 DBREF 6LOJ B 1 592 UNP P32455 GBP1_HUMAN 1 592 SEQADV 6LOJ ASP A 19 UNP A0A380D7J EXPRESSION TAG SEQADV 6LOJ PRO A 20 UNP A0A380D7J EXPRESSION TAG SEQADV 6LOJ SER A 21 UNP A0A380D7J EXPRESSION TAG SEQADV 6LOJ MET B -2 UNP P32455 EXPRESSION TAG SEQADV 6LOJ ASP B -1 UNP P32455 EXPRESSION TAG SEQADV 6LOJ PRO B 0 UNP P32455 EXPRESSION TAG SEQADV 6LOJ HIS B 507 UNP P32455 GLN 507 ENGINEERED MUTATION SEQRES 1 A 226 ASP PRO SER THR TYR ALA ASP TYR PHE SER ALA TRP ASP SEQRES 2 A 226 LYS TRP GLU LYS GLN ALA LEU PRO GLY GLU GLU ARG ASP SEQRES 3 A 226 GLU ALA VAL SER ARG LEU LYS GLU CYS LEU ILE ASN ASN SEQRES 4 A 226 SER ASP GLU LEU ARG LEU ASP ARG LEU ASN LEU SER SER SEQRES 5 A 226 LEU PRO ASP ASN LEU PRO ALA GLN ILE THR LEU LEU ASN SEQRES 6 A 226 VAL SER TYR ASN GLN LEU THR ASN LEU PRO GLU LEU PRO SEQRES 7 A 226 VAL THR LEU LYS LYS LEU TYR SER ALA SER ASN LYS LEU SEQRES 8 A 226 SER GLU LEU PRO VAL LEU PRO PRO ALA LEU GLU SER LEU SEQRES 9 A 226 GLN VAL GLN HIS ASN GLU LEU GLU ASN LEU PRO ALA LEU SEQRES 10 A 226 PRO ASP SER LEU LEU THR MET ASN ILE SER TYR ASN GLU SEQRES 11 A 226 ILE VAL SER LEU PRO SER LEU PRO GLN ALA LEU LYS ASN SEQRES 12 A 226 LEU ARG ALA THR ARG ASN PHE LEU THR GLU LEU PRO ALA SEQRES 13 A 226 PHE SER GLU GLY ASN ASN PRO VAL VAL ARG GLU TYR PHE SEQRES 14 A 226 PHE ASP ARG ASN GLN ILE SER HIS ILE PRO GLU SER ILE SEQRES 15 A 226 LEU ASN LEU ARG ASN GLU CYS SER ILE HIS ILE SER ASP SEQRES 16 A 226 ASN PRO LEU SER SER HIS ALA LEU GLN ALA LEU GLN ARG SEQRES 17 A 226 LEU THR SER SER PRO ASP TYR HIS GLY PRO ARG ILE TYR SEQRES 18 A 226 PHE SER MET SER ASP SEQRES 1 B 595 MET ASP PRO MET ALA SER GLU ILE HIS MET THR GLY PRO SEQRES 2 B 595 MET CYS LEU ILE GLU ASN THR ASN GLY ARG LEU MET ALA SEQRES 3 B 595 ASN PRO GLU ALA LEU LYS ILE LEU SER ALA ILE THR GLN SEQRES 4 B 595 PRO MET VAL VAL VAL ALA ILE VAL GLY LEU TYR ARG THR SEQRES 5 B 595 GLY LYS SER TYR LEU MET ASN LYS LEU ALA GLY LYS LYS SEQRES 6 B 595 LYS GLY PHE SER LEU GLY SER THR VAL GLN SER HIS THR SEQRES 7 B 595 LYS GLY ILE TRP MET TRP CYS VAL PRO HIS PRO LYS LYS SEQRES 8 B 595 PRO GLY HIS ILE LEU VAL LEU LEU ASP THR GLU GLY LEU SEQRES 9 B 595 GLY ASP VAL GLU LYS GLY ASP ASN GLN ASN ASP SER TRP SEQRES 10 B 595 ILE PHE ALA LEU ALA VAL LEU LEU SER SER THR PHE VAL SEQRES 11 B 595 TYR ASN SER ILE GLY THR ILE ASN GLN GLN ALA MET ASP SEQRES 12 B 595 GLN LEU TYR TYR VAL THR GLU LEU THR HIS ARG ILE ARG SEQRES 13 B 595 SER LYS SER SER PRO ASP GLU ASN GLU ASN GLU VAL GLU SEQRES 14 B 595 ASP SER ALA ASP PHE VAL SER PHE PHE PRO ASP PHE VAL SEQRES 15 B 595 TRP THR LEU ARG ASP PHE SER LEU ASP LEU GLU ALA ASP SEQRES 16 B 595 GLY GLN PRO LEU THR PRO ASP GLU TYR LEU THR TYR SER SEQRES 17 B 595 LEU LYS LEU LYS LYS GLY THR SER GLN LYS ASP GLU THR SEQRES 18 B 595 PHE ASN LEU PRO ARG LEU CYS ILE ARG LYS PHE PHE PRO SEQRES 19 B 595 LYS LYS LYS CYS PHE VAL PHE ASP ARG PRO VAL HIS ARG SEQRES 20 B 595 ARG LYS LEU ALA GLN LEU GLU LYS LEU GLN ASP GLU GLU SEQRES 21 B 595 LEU ASP PRO GLU PHE VAL GLN GLN VAL ALA ASP PHE CYS SEQRES 22 B 595 SER TYR ILE PHE SER ASN SER LYS THR LYS THR LEU SER SEQRES 23 B 595 GLY GLY ILE GLN VAL ASN GLY PRO ARG LEU GLU SER LEU SEQRES 24 B 595 VAL LEU THR TYR VAL ASN ALA ILE SER SER GLY ASP LEU SEQRES 25 B 595 PRO CYS MET GLU ASN ALA VAL LEU ALA LEU ALA GLN ILE SEQRES 26 B 595 GLU ASN SER ALA ALA VAL GLN LYS ALA ILE ALA HIS TYR SEQRES 27 B 595 GLU GLN GLN MET GLY GLN LYS VAL GLN LEU PRO THR GLU SEQRES 28 B 595 THR LEU GLN GLU LEU LEU ASP LEU HIS ARG ASP SER GLU SEQRES 29 B 595 ARG GLU ALA ILE GLU VAL PHE ILE ARG SER SER PHE LYS SEQRES 30 B 595 ASP VAL ASP HIS LEU PHE GLN LYS GLU LEU ALA ALA GLN SEQRES 31 B 595 LEU GLU LYS LYS ARG ASP ASP PHE CYS LYS GLN ASN GLN SEQRES 32 B 595 GLU ALA SER SER ASP ARG CYS SER ALA LEU LEU GLN VAL SEQRES 33 B 595 ILE PHE SER PRO LEU GLU GLU GLU VAL LYS ALA GLY ILE SEQRES 34 B 595 TYR SER LYS PRO GLY GLY TYR ARG LEU PHE VAL GLN LYS SEQRES 35 B 595 LEU GLN ASP LEU LYS LYS LYS TYR TYR GLU GLU PRO ARG SEQRES 36 B 595 LYS GLY ILE GLN ALA GLU GLU ILE LEU GLN THR TYR LEU SEQRES 37 B 595 LYS SER LYS GLU SER MET THR ASP ALA ILE LEU GLN THR SEQRES 38 B 595 ASP GLN THR LEU THR GLU LYS GLU LYS GLU ILE GLU VAL SEQRES 39 B 595 GLU ARG VAL LYS ALA GLU SER ALA GLN ALA SER ALA LYS SEQRES 40 B 595 MET LEU HIS GLU MET GLN ARG LYS ASN GLU GLN MET MET SEQRES 41 B 595 GLU GLN LYS GLU ARG SER TYR GLN GLU HIS LEU LYS GLN SEQRES 42 B 595 LEU THR GLU LYS MET GLU ASN ASP ARG VAL GLN LEU LEU SEQRES 43 B 595 LYS GLU GLN GLU ARG THR LEU ALA LEU LYS LEU GLN GLU SEQRES 44 B 595 GLN GLU GLN LEU LEU LYS GLU GLY PHE GLN LYS GLU SER SEQRES 45 B 595 ARG ILE MET LYS ASN GLU ILE GLN ASP LEU GLN THR LYS SEQRES 46 B 595 MET ARG ARG ARG LYS ALA CYS THR ILE SER HET GDP B 601 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 3 GDP C10 H15 N5 O11 P2 HELIX 1 AA1 THR A 22 GLN A 36 1 15 HELIX 2 AA2 GLU A 42 ASN A 57 1 16 HELIX 3 AA3 PRO A 197 ASN A 202 1 6 HELIX 4 AA4 SER A 217 SER A 229 1 13 HELIX 5 AA5 ASN B 24 SER B 32 1 9 HELIX 6 AA6 LYS B 51 GLY B 60 1 10 HELIX 7 AA7 ASP B 108 GLN B 110 5 3 HELIX 8 AA8 ASN B 111 SER B 123 1 13 HELIX 9 AA9 ASN B 135 LEU B 142 1 8 HELIX 10 AB1 TYR B 143 ILE B 152 1 10 HELIX 11 AB2 ASP B 167 ALA B 169 5 3 HELIX 12 AB3 ASP B 170 PHE B 175 1 6 HELIX 13 AB4 THR B 197 LEU B 206 1 10 HELIX 14 AB5 SER B 213 PHE B 229 1 17 HELIX 15 AB6 LYS B 252 GLU B 257 1 6 HELIX 16 AB7 PHE B 262 SER B 277 1 16 HELIX 17 AB8 ASN B 289 SER B 306 1 18 HELIX 18 AB9 CYS B 311 VAL B 343 1 33 HELIX 19 AC1 LEU B 350 SER B 372 1 23 HELIX 20 AC2 ASP B 375 ASP B 377 5 3 HELIX 21 AC3 HIS B 378 PHE B 415 1 38 HELIX 22 AC4 PHE B 415 ALA B 424 1 10 HELIX 23 AC5 GLY B 431 GLU B 450 1 20 HELIX 24 AC6 GLN B 456 LYS B 466 1 11 HELIX 25 AC7 LYS B 468 LEU B 476 1 9 HELIX 26 AC8 GLU B 488 GLU B 563 1 76 HELIX 27 AC9 PHE B 565 ARG B 584 1 20 SHEET 1 AA1 5 GLU A 60 ARG A 62 0 SHEET 2 AA1 5 LEU A 81 ASN A 83 1 O ASN A 83 N LEU A 61 SHEET 3 AA1 5 LYS A 101 TYR A 103 1 O TYR A 103 N LEU A 82 SHEET 4 AA1 5 SER A 121 GLN A 123 1 O GLN A 123 N LEU A 102 SHEET 5 AA1 5 THR A 141 ASN A 143 1 O ASN A 143 N LEU A 122 SHEET 1 AA2 4 LEU A 162 ARG A 163 0 SHEET 2 AA2 4 GLU A 185 PHE A 187 1 O PHE A 187 N LEU A 162 SHEET 3 AA2 4 SER A 208 HIS A 210 1 O SER A 208 N TYR A 186 SHEET 4 AA2 4 ARG A 237 TYR A 239 1 O ARG A 237 N ILE A 209 SHEET 1 AA3 8 ARG B 20 ALA B 23 0 SHEET 2 AA3 8 MET B 11 THR B 17 -1 N THR B 17 O ARG B 20 SHEET 3 AA3 8 ILE B 78 PRO B 84 -1 O MET B 80 N MET B 11 SHEET 4 AA3 8 ILE B 92 ASP B 97 -1 O ASP B 97 N TRP B 79 SHEET 5 AA3 8 MET B 38 GLY B 45 1 N VAL B 41 O VAL B 94 SHEET 6 AA3 8 THR B 125 SER B 130 1 O VAL B 127 N ALA B 42 SHEET 7 AA3 8 ASP B 177 LEU B 182 1 O VAL B 179 N TYR B 128 SHEET 8 AA3 8 LYS B 233 VAL B 237 1 O PHE B 236 N LEU B 182 SHEET 1 AA4 2 THR B 281 LEU B 282 0 SHEET 2 AA4 2 ILE B 286 GLN B 287 -1 N ILE B 286 O LEU B 282 CISPEP 1 LEU B 345 PRO B 346 0 -2.96 SITE 1 AC1 11 TYR B 47 ARG B 48 THR B 49 GLY B 50 SITE 2 AC1 11 LYS B 51 SER B 52 THR B 98 GLU B 99 SITE 3 AC1 11 GLY B 100 ASP B 184 ALA B 248 CRYST1 122.490 122.490 582.350 90.00 90.00 120.00 P 61 2 2 12 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 0.008164 0.004713 0.000000 0.00000 SCALE2 0.000000 0.009427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.001717 0.00000