PDB Short entry for 2D4H HEADER SIGNALING PROTEIN 19-OCT-05 2D4H TITLE CRYSTAL-STRUCTURE OF THE N-TERMINAL LARGE GTPASE DOMAIN OF HUMAN TITLE 2 GUANYLATE BINDING PROTEIN 1 (HGBP1) IN COMPLEX WITH GMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON-INDUCED GUANYLATE-BINDING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL LARGE GTPASE DOMAIN; COMPND 5 SYNONYM: GTP-BINDING PROTEIN 1, GUANINE NUCLEOTIDE-BINDING PROTEIN 1, COMPND 6 HUGBP-1; COMPND 7 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: GBP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE9 KEYWDS PROTEIN- GUANINE NUCLEOTIDE COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GHOSH,G.J.K.PRAEFCKE,L.RENAULT,A.WITTINGHOFER,C.HERRMANN REVDAT 6 23-AUG-23 2D4H 1 REMARK SEQADV LINK REVDAT 5 24-JAN-18 2D4H 1 AUTHOR REVDAT 4 11-OCT-17 2D4H 1 REMARK REVDAT 3 13-JUL-11 2D4H 1 VERSN REVDAT 2 24-FEB-09 2D4H 1 VERSN REVDAT 1 07-MAR-06 2D4H 0 JRNL AUTH A.GHOSH,G.J.PRAEFCKE,L.RENAULT,A.WITTINGHOFER,C.HERRMANN JRNL TITL HOW GUANYLATE-BINDING PROTEINS ACHIEVE ASSEMBLY-STIMULATED JRNL TITL 2 PROCESSIVE CLEAVAGE OF GTP TO GMP. JRNL REF NATURE V. 440 101 2006 JRNL REFN ISSN 0028-0836 JRNL PMID 16511497 JRNL DOI 10.1038/NATURE04510 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.PRAKASH,L.RENAULT,G.J.PRAEFCKE,C.HERRMANN,A.WITTINGHOFER REMARK 1 TITL TRIPHOSPHATE STRUCTURE OF GUANYLATE-BINDING PROTEIN 1 AND REMARK 1 TITL 2 IMPLICATIONS FOR NUCLEOTIDE BINDING AND GTPASE MECHANISM. REMARK 1 REF EMBO J. V. 19 4555 2000 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 10970849 REMARK 1 DOI 10.1093/EMBOJ/19.17.4555 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.PRAKASH,G.J.PRAEFCKE,L.RENAULT,C.HERRMANN,A.WITTINGHOFER REMARK 1 TITL STRUCTURE OF HUMAN GUANYLATE-BINDING PROTEIN 1 REPRESENTING REMARK 1 TITL 2 A UNIQUE CLASS OF GTP-BINDING PROTEINS. REMARK 1 REF NATURE V. 403 567 2000 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 10676968 REMARK 1 DOI 10.1038/35000617 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 13093 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 718 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 939 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.3570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4611 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -1.38000 REMARK 3 B33 (A**2) : 1.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.492 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.370 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.337 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.888 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4762 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6447 ; 0.964 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 575 ; 4.111 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 730 ; 0.055 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3498 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2414 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 202 ; 0.127 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 92 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.143 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2902 ; 0.628 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4699 ; 1.164 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1860 ; 0.854 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1748 ; 1.592 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 7 A 313 4 REMARK 3 1 B 7 B 311 4 REMARK 3 2 A 593 A 593 1 REMARK 3 2 B 593 B 593 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 33 ; 0.09 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 4302 ; 0.74 ; 0.50 REMARK 3 TIGHT THERMAL 1 A (A**2): 33 ; 0.25 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 4302 ; 3.07 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 316 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3715 0.5149 15.1662 REMARK 3 T TENSOR REMARK 3 T11: 0.0135 T22: 0.0841 REMARK 3 T33: 0.0341 T12: 0.0050 REMARK 3 T13: 0.0166 T23: 0.0071 REMARK 3 L TENSOR REMARK 3 L11: 1.1875 L22: 1.0743 REMARK 3 L33: 0.5463 L12: 0.1558 REMARK 3 L13: 0.2151 L23: 0.0098 REMARK 3 S TENSOR REMARK 3 S11: -0.0164 S12: -0.0012 S13: 0.0125 REMARK 3 S21: 0.0372 S22: 0.0074 S23: 0.0028 REMARK 3 S31: -0.0026 S32: -0.0314 S33: 0.0090 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 7 B 311 REMARK 3 ORIGIN FOR THE GROUP (A): 5.9897 44.7562 5.5610 REMARK 3 T TENSOR REMARK 3 T11: 0.0541 T22: 0.0598 REMARK 3 T33: 0.0550 T12: 0.0398 REMARK 3 T13: -0.0036 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.2801 L22: 2.0009 REMARK 3 L33: 1.1923 L12: -0.1982 REMARK 3 L13: -0.0306 L23: -0.2346 REMARK 3 S TENSOR REMARK 3 S11: -0.0348 S12: -0.0772 S13: 0.0128 REMARK 3 S21: -0.0226 S22: 0.0262 S23: -0.0022 REMARK 3 S31: 0.1438 S32: -0.0608 S33: 0.0086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D4H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-05. REMARK 100 THE DEPOSITION ID IS D_1000024975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980 REMARK 200 MONOCHROMATOR : MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14479 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY: 2B8W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 130 MM NH4NO3, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 86.72500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: TWO BIOLOGICAL ASSEMBLIES ARE IN THE ASYMMETRIC UNIT 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 MET A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 GLU A 4 REMARK 465 SER A 73 REMARK 465 HIS A 74 REMARK 465 THR A 75 REMARK 465 LYS A 106 REMARK 465 GLY A 107 REMARK 465 ASP A 108 REMARK 465 ASN A 161 REMARK 465 GLU A 162 REMARK 465 ASN A 163 REMARK 465 GLU A 164 REMARK 465 VAL A 165 REMARK 465 GLU A 166 REMARK 465 ASP A 167 REMARK 465 LEU A 317 REMARK 465 MET B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 MET B -3 REMARK 465 ARG B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 ILE B 5 REMARK 465 THR B 70 REMARK 465 VAL B 71 REMARK 465 GLN B 72 REMARK 465 SER B 73 REMARK 465 HIS B 74 REMARK 465 THR B 75 REMARK 465 ASP B 103 REMARK 465 VAL B 104 REMARK 465 GLU B 105 REMARK 465 LYS B 106 REMARK 465 GLY B 107 REMARK 465 ASP B 108 REMARK 465 ASN B 109 REMARK 465 PRO B 158 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 MET B 312 REMARK 465 GLU B 313 REMARK 465 ASN B 314 REMARK 465 ALA B 315 REMARK 465 VAL B 316 REMARK 465 LEU B 317 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 GLN B 110 CG CD OE1 NE2 REMARK 470 SER B 157 OG 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 ASP A 216 CB - CG - OD2 ANGL. DEV. = 5.6 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 HIS A 6 -57.58 -1.40 REMARK 500 MET A 7 90.63 -15.23 REMARK 500 VAL A 71 -79.35 -68.75 REMARK 500 LEU A 101 109.35 -56.30 REMARK 500 GLN A 110 93.00 -65.65 REMARK 500 ASN A 111 23.68 -76.26 REMARK 500 ASP A 184 17.67 45.29 REMARK 500 PHE A 185 49.22 -102.58 REMARK 500 LEU A 187 -85.59 -68.22 REMARK 500 ASP A 188 65.85 35.41 REMARK 500 ASP A 192 -61.64 -108.89 REMARK 500 THR A 212 45.26 -83.23 REMARK 500 THR A 218 36.64 -77.05 REMARK 500 PHE A 219 -35.60 -142.45 REMARK 500 LYS A 246 87.55 -64.27 REMARK 500 ALA A 248 105.30 59.00 REMARK 500 LEU A 250 45.71 79.53 REMARK 500 ASP A 308 -83.00 -93.27 REMARK 500 LEU A 309 105.31 62.09 REMARK 500 ASN B 16 45.98 -95.40 REMARK 500 THR B 17 87.49 -67.69 REMARK 500 ASN B 18 94.05 55.12 REMARK 500 ALA B 33 39.73 -93.09 REMARK 500 LYS B 63 -124.14 -78.05 REMARK 500 LEU B 101 18.35 -146.38 REMARK 500 SER B 168 -94.18 -78.86 REMARK 500 ALA B 169 -27.00 -172.59 REMARK 500 SER B 186 85.86 179.03 REMARK 500 LEU B 187 -161.56 -74.51 REMARK 500 LEU B 189 116.00 74.97 REMARK 500 THR B 218 1.43 -69.08 REMARK 500 PHE B 230 79.88 -119.29 REMARK 500 ARG B 245 126.58 -2.32 REMARK 500 SER B 283 -66.41 -27.18 REMARK 500 ASN B 289 -166.24 -121.48 REMARK 500 SER B 305 34.60 -83.58 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 5GP A 593 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP B 593 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B8W RELATED DB: PDB REMARK 900 SAME PROTEIN (N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GMP/ REMARK 900 ALF4 REMARK 900 RELATED ID: 2B92 RELATED DB: PDB REMARK 900 SAME PROTEIN (N-TERMINAL LARGE GTPASE DOMAIN) IN COMPLEX WITH GDP/ REMARK 900 ALF3 REMARK 900 RELATED ID: 1DG3 RELATED DB: PDB REMARK 900 THE FULL LENGTH PROTEIN WITH H507Q MUTATION AND IN NUCLEOTIDE FREE REMARK 900 STATE REMARK 900 RELATED ID: 1F5N RELATED DB: PDB REMARK 900 THE FULL LENGTH PROTEIN WITH H507Q MUTATION AND IN COMPLEX WITH NON- REMARK 900 HYDROLYSABLE GTP ANALOGUE GPPNHP DBREF 2D4H A 1 317 UNP P32455 GBP1_HUMAN 1 317 DBREF 2D4H B 1 317 UNP P32455 GBP1_HUMAN 1 317 SEQADV 2D4H MET A -10 UNP P32455 CLONING ARTIFACT SEQADV 2D4H HIS A -9 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS A -8 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS A -7 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS A -6 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS A -5 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS A -4 UNP P32455 EXPRESSION TAG SEQADV 2D4H MET A -3 UNP P32455 CLONING ARTIFACT SEQADV 2D4H ARG A -2 UNP P32455 CLONING ARTIFACT SEQADV 2D4H GLY A -1 UNP P32455 CLONING ARTIFACT SEQADV 2D4H SER A 0 UNP P32455 CLONING ARTIFACT SEQADV 2D4H MET B -10 UNP P32455 CLONING ARTIFACT SEQADV 2D4H HIS B -9 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS B -8 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS B -7 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS B -6 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS B -5 UNP P32455 EXPRESSION TAG SEQADV 2D4H HIS B -4 UNP P32455 EXPRESSION TAG SEQADV 2D4H MET B -3 UNP P32455 CLONING ARTIFACT SEQADV 2D4H ARG B -2 UNP P32455 CLONING ARTIFACT SEQADV 2D4H GLY B -1 UNP P32455 CLONING ARTIFACT SEQADV 2D4H SER B 0 UNP P32455 CLONING ARTIFACT SEQRES 1 A 328 MET HIS HIS HIS HIS HIS HIS MET ARG GLY SER MET ALA SEQRES 2 A 328 SER GLU ILE HIS MET THR GLY PRO MET CYS LEU ILE GLU SEQRES 3 A 328 ASN THR ASN GLY ARG LEU MET ALA ASN PRO GLU ALA LEU SEQRES 4 A 328 LYS ILE LEU SER ALA ILE THR GLN PRO MET VAL VAL VAL SEQRES 5 A 328 ALA ILE VAL GLY LEU TYR ARG THR GLY LYS SER TYR LEU SEQRES 6 A 328 MET ASN LYS LEU ALA GLY LYS LYS LYS GLY PHE SER LEU SEQRES 7 A 328 GLY SER THR VAL GLN SER HIS THR LYS GLY ILE TRP MET SEQRES 8 A 328 TRP CYS VAL PRO HIS PRO LYS LYS PRO GLY HIS ILE LEU SEQRES 9 A 328 VAL LEU LEU ASP THR GLU GLY LEU GLY ASP VAL GLU LYS SEQRES 10 A 328 GLY ASP ASN GLN ASN ASP SER TRP ILE PHE ALA LEU ALA SEQRES 11 A 328 VAL LEU LEU SER SER THR PHE VAL TYR ASN SER ILE GLY SEQRES 12 A 328 THR ILE ASN GLN GLN ALA MET ASP GLN LEU TYR TYR VAL SEQRES 13 A 328 THR GLU LEU THR HIS ARG ILE ARG SER LYS SER SER PRO SEQRES 14 A 328 ASP GLU ASN GLU ASN GLU VAL GLU ASP SER ALA ASP PHE SEQRES 15 A 328 VAL SER PHE PHE PRO ASP PHE VAL TRP THR LEU ARG ASP SEQRES 16 A 328 PHE SER LEU ASP LEU GLU ALA ASP GLY GLN PRO LEU THR SEQRES 17 A 328 PRO ASP GLU TYR LEU THR TYR SER LEU LYS LEU LYS LYS SEQRES 18 A 328 GLY THR SER GLN LYS ASP GLU THR PHE ASN LEU PRO ARG SEQRES 19 A 328 LEU CYS ILE ARG LYS PHE PHE PRO LYS LYS LYS CYS PHE SEQRES 20 A 328 VAL PHE ASP ARG PRO VAL HIS ARG ARG LYS LEU ALA GLN SEQRES 21 A 328 LEU GLU LYS LEU GLN ASP GLU GLU LEU ASP PRO GLU PHE SEQRES 22 A 328 VAL GLN GLN VAL ALA ASP PHE CYS SER TYR ILE PHE SER SEQRES 23 A 328 ASN SER LYS THR LYS THR LEU SER GLY GLY ILE GLN VAL SEQRES 24 A 328 ASN GLY PRO ARG LEU GLU SER LEU VAL LEU THR TYR VAL SEQRES 25 A 328 ASN ALA ILE SER SER GLY ASP LEU PRO CYS MET GLU ASN SEQRES 26 A 328 ALA VAL LEU SEQRES 1 B 328 MET HIS HIS HIS HIS HIS HIS MET ARG GLY SER MET ALA SEQRES 2 B 328 SER GLU ILE HIS MET THR GLY PRO MET CYS LEU ILE GLU SEQRES 3 B 328 ASN THR ASN GLY ARG LEU MET ALA ASN PRO GLU ALA LEU SEQRES 4 B 328 LYS ILE LEU SER ALA ILE THR GLN PRO MET VAL VAL VAL SEQRES 5 B 328 ALA ILE VAL GLY LEU TYR ARG THR GLY LYS SER TYR LEU SEQRES 6 B 328 MET ASN LYS LEU ALA GLY LYS LYS LYS GLY PHE SER LEU SEQRES 7 B 328 GLY SER THR VAL GLN SER HIS THR LYS GLY ILE TRP MET SEQRES 8 B 328 TRP CYS VAL PRO HIS PRO LYS LYS PRO GLY HIS ILE LEU SEQRES 9 B 328 VAL LEU LEU ASP THR GLU GLY LEU GLY ASP VAL GLU LYS SEQRES 10 B 328 GLY ASP ASN GLN ASN ASP SER TRP ILE PHE ALA LEU ALA SEQRES 11 B 328 VAL LEU LEU SER SER THR PHE VAL TYR ASN SER ILE GLY SEQRES 12 B 328 THR ILE ASN GLN GLN ALA MET ASP GLN LEU TYR TYR VAL SEQRES 13 B 328 THR GLU LEU THR HIS ARG ILE ARG SER LYS SER SER PRO SEQRES 14 B 328 ASP GLU ASN GLU ASN GLU VAL GLU ASP SER ALA ASP PHE SEQRES 15 B 328 VAL SER PHE PHE PRO ASP PHE VAL TRP THR LEU ARG ASP SEQRES 16 B 328 PHE SER LEU ASP LEU GLU ALA ASP GLY GLN PRO LEU THR SEQRES 17 B 328 PRO ASP GLU TYR LEU THR TYR SER LEU LYS LEU LYS LYS SEQRES 18 B 328 GLY THR SER GLN LYS ASP GLU THR PHE ASN LEU PRO ARG SEQRES 19 B 328 LEU CYS ILE ARG LYS PHE PHE PRO LYS LYS LYS CYS PHE SEQRES 20 B 328 VAL PHE ASP ARG PRO VAL HIS ARG ARG LYS LEU ALA GLN SEQRES 21 B 328 LEU GLU LYS LEU GLN ASP GLU GLU LEU ASP PRO GLU PHE SEQRES 22 B 328 VAL GLN GLN VAL ALA ASP PHE CYS SER TYR ILE PHE SER SEQRES 23 B 328 ASN SER LYS THR LYS THR LEU SER GLY GLY ILE GLN VAL SEQRES 24 B 328 ASN GLY PRO ARG LEU GLU SER LEU VAL LEU THR TYR VAL SEQRES 25 B 328 ASN ALA ILE SER SER GLY ASP LEU PRO CYS MET GLU ASN SEQRES 26 B 328 ALA VAL LEU HET 5GP A 593 24 HET 5GP B 593 24 HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE FORMUL 3 5GP 2(C10 H14 N5 O8 P) FORMUL 5 HOH *119(H2 O) HELIX 1 1 ASN A 24 ILE A 34 1 11 HELIX 2 2 GLY A 50 GLY A 60 1 11 HELIX 3 3 ASN A 111 SER A 123 1 13 HELIX 4 4 ASN A 135 LYS A 155 1 21 HELIX 5 5 THR A 197 LEU A 206 1 10 HELIX 6 6 ASP A 216 PHE A 230 1 15 HELIX 7 7 GLN A 254 LEU A 258 5 5 HELIX 8 8 ASP A 259 SER A 277 1 19 HELIX 9 9 ASN A 289 SER A 306 1 18 HELIX 10 10 ASN B 24 ALA B 33 1 10 HELIX 11 11 GLY B 50 ALA B 59 1 10 HELIX 12 12 ASN B 111 SER B 123 1 13 HELIX 13 13 ASN B 135 SER B 156 1 22 HELIX 14 14 THR B 197 LEU B 206 1 10 HELIX 15 15 SER B 213 PHE B 230 1 18 HELIX 16 16 GLN B 254 LEU B 258 5 5 HELIX 17 17 ASP B 259 SER B 277 1 19 HELIX 18 18 ASN B 289 SER B 305 1 17 SHEET 1 A 8 ARG A 20 ALA A 23 0 SHEET 2 A 8 MET A 11 THR A 17 -1 N GLU A 15 O MET A 22 SHEET 3 A 8 GLY A 77 PRO A 84 -1 O MET A 80 N MET A 11 SHEET 4 A 8 ILE A 92 GLU A 99 -1 O LEU A 93 N VAL A 83 SHEET 5 A 8 MET A 38 GLY A 45 1 N ILE A 43 O LEU A 96 SHEET 6 A 8 THR A 125 ILE A 131 1 O VAL A 127 N VAL A 44 SHEET 7 A 8 ASP A 177 ARG A 183 1 O ASP A 177 N PHE A 126 SHEET 8 A 8 LYS A 233 VAL A 237 1 O PHE A 236 N LEU A 182 SHEET 1 B 2 PHE A 65 SER A 66 0 SHEET 2 B 2 LYS A 252 LEU A 253 -1 O LEU A 253 N PHE A 65 SHEET 1 C 8 MET B 22 ALA B 23 0 SHEET 2 C 8 MET B 11 GLU B 15 -1 N GLU B 15 O MET B 22 SHEET 3 C 8 GLY B 77 PRO B 84 -1 O MET B 80 N MET B 11 SHEET 4 C 8 ILE B 92 GLU B 99 -1 O LEU B 93 N VAL B 83 SHEET 5 C 8 MET B 38 GLY B 45 1 N ILE B 43 O LEU B 96 SHEET 6 C 8 THR B 125 ILE B 131 1 O ASN B 129 N VAL B 44 SHEET 7 C 8 ASP B 177 ARG B 183 1 O THR B 181 N TYR B 128 SHEET 8 C 8 LYS B 233 VAL B 237 1 O PHE B 236 N LEU B 182 SHEET 1 D 2 PHE B 65 SER B 66 0 SHEET 2 D 2 LYS B 252 LEU B 253 -1 O LEU B 253 N PHE B 65 LINK OD2 ASP A 184 N2 5GP A 593 1555 1555 2.47 LINK OD2 ASP B 184 N2 5GP B 593 1555 1555 2.69 SITE 1 AC1 13 ARG A 48 THR A 49 GLY A 50 LYS A 51 SITE 2 AC1 13 SER A 52 PHE A 65 SER A 66 GLY A 68 SITE 3 AC1 13 ARG A 183 ASP A 184 PRO A 241 HOH A 599 SITE 4 AC1 13 HOH A 606 SITE 1 AC2 15 ARG B 48 THR B 49 GLY B 50 LYS B 51 SITE 2 AC2 15 SER B 52 PHE B 65 SER B 66 GLY B 68 SITE 3 AC2 15 ILE B 131 ARG B 183 ASP B 184 PRO B 241 SITE 4 AC2 15 HOH B 598 HOH B 640 HOH B 649 CRYST1 39.921 173.450 49.632 90.00 110.85 90.00 P 1 21 1 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 0.025049 0.000000 0.009539 0.00000 SCALE2 0.000000 0.005765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021560 0.00000