PDB Short entry for 1MHQ HEADER PROTEIN TRANSPORT 20-AUG-02 1MHQ TITLE CRYSTAL STRUCTURE OF HUMAN GGA2 VHS DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: VHS DOMAIN (N-TERMINAL DOMAIN); COMPND 5 SYNONYM: GOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF-BINDING PROTEIN COMPND 6 2; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS SUPER HELIX, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHU,X.C.ZHANG REVDAT 3 11-OCT-17 1MHQ 1 REMARK REVDAT 2 24-FEB-09 1MHQ 1 VERSN REVDAT 1 11-MAR-03 1MHQ 0 JRNL AUTH G.ZHU,X.HE,S.TERZYAN,P.ZHAI,J.TANG,X.C.ZHANG JRNL TITL CRYSTAL STRUCTURE OF GGA2 VHS DOMAIN AND ITS IMPLICATION IN JRNL TITL 2 PLASTICITY IN THE LIGAND BINDING POCKET JRNL REF FEBS LETT. V. 537 171 2003 JRNL REFN ISSN 0014-5793 JRNL PMID 12606052 JRNL DOI 10.1016/S0014-5793(03)00095-4 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 15117 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 737 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 69.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 88 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.032 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2329 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.30 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.34 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.38 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.060 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.252 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.366 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.731 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.173 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MHQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-AUG-02. REMARK 100 THE DEPOSITION ID IS D_1000016919. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.43800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, ISO-PROPANOL, BETA REMARK 280 -MERCAPTOETHANOL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 31.43000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.05500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.43000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.05500 REMARK 290 SMTRY3 4 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 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 PRO A 168 REMARK 465 VAL A 169 REMARK 465 ASP A 170 REMARK 465 LYS A 171 REMARK 465 ILE A 172 REMARK 465 LYS B 117 REMARK 465 TYR B 118 REMARK 465 LYS B 171 REMARK 465 ILE B 172 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LEU B 119 CB CG CD1 CD2 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 LYS A 166 -140.33 -87.27 REMARK 500 ASP B 56 124.00 168.36 REMARK 500 GLN B 163 116.41 45.96 REMARK 500 ASP B 164 177.81 173.10 REMARK 500 PRO B 165 -149.64 -85.80 REMARK 500 LEU B 167 68.34 -166.27 REMARK 500 PRO B 168 116.04 -31.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 1MHQ A 25 172 UNP Q9UJY4 GGA2_HUMAN 25 172 DBREF 1MHQ B 25 172 UNP Q9UJY4 GGA2_HUMAN 25 172 SEQRES 1 A 148 SER LEU GLU LEU TRP LEU ASN LYS ALA THR ASP PRO SER SEQRES 2 A 148 MET SER GLU GLN ASP TRP SER ALA ILE GLN ASN PHE CYS SEQRES 3 A 148 GLU GLN VAL ASN THR ASP PRO ASN GLY PRO THR HIS ALA SEQRES 4 A 148 PRO TRP LEU LEU ALA HIS LYS ILE GLN SER PRO GLN GLU SEQRES 5 A 148 LYS GLU ALA LEU TYR ALA LEU THR VAL LEU GLU MET CYS SEQRES 6 A 148 MET ASN HIS CYS GLY GLU LYS PHE HIS SER GLU VAL ALA SEQRES 7 A 148 LYS PHE ARG PHE LEU ASN GLU LEU ILE LYS VAL LEU SER SEQRES 8 A 148 PRO LYS TYR LEU GLY SER TRP ALA THR GLY LYS VAL LYS SEQRES 9 A 148 GLY ARG VAL ILE GLU ILE LEU PHE SER TRP THR VAL TRP SEQRES 10 A 148 PHE PRO GLU ASP ILE LYS ILE ARG ASP ALA TYR GLN MET SEQRES 11 A 148 LEU LYS LYS GLN GLY ILE ILE LYS GLN ASP PRO LYS LEU SEQRES 12 A 148 PRO VAL ASP LYS ILE SEQRES 1 B 148 SER LEU GLU LEU TRP LEU ASN LYS ALA THR ASP PRO SER SEQRES 2 B 148 MET SER GLU GLN ASP TRP SER ALA ILE GLN ASN PHE CYS SEQRES 3 B 148 GLU GLN VAL ASN THR ASP PRO ASN GLY PRO THR HIS ALA SEQRES 4 B 148 PRO TRP LEU LEU ALA HIS LYS ILE GLN SER PRO GLN GLU SEQRES 5 B 148 LYS GLU ALA LEU TYR ALA LEU THR VAL LEU GLU MET CYS SEQRES 6 B 148 MET ASN HIS CYS GLY GLU LYS PHE HIS SER GLU VAL ALA SEQRES 7 B 148 LYS PHE ARG PHE LEU ASN GLU LEU ILE LYS VAL LEU SER SEQRES 8 B 148 PRO LYS TYR LEU GLY SER TRP ALA THR GLY LYS VAL LYS SEQRES 9 B 148 GLY ARG VAL ILE GLU ILE LEU PHE SER TRP THR VAL TRP SEQRES 10 B 148 PHE PRO GLU ASP ILE LYS ILE ARG ASP ALA TYR GLN MET SEQRES 11 B 148 LEU LYS LYS GLN GLY ILE ILE LYS GLN ASP PRO LYS LEU SEQRES 12 B 148 PRO VAL ASP LYS ILE FORMUL 3 HOH *104(H2 O) HELIX 1 1 SER A 25 ASP A 35 1 11 HELIX 2 2 ASP A 42 ASP A 56 1 15 HELIX 3 3 PRO A 57 GLN A 72 1 16 HELIX 4 4 GLN A 75 CYS A 93 1 19 HELIX 5 5 GLY A 94 ALA A 102 1 9 HELIX 6 6 LYS A 103 VAL A 113 1 11 HELIX 7 7 THR A 124 PHE A 142 1 19 HELIX 8 8 ASP A 145 GLN A 158 1 14 HELIX 9 9 SER B 25 THR B 34 1 10 HELIX 10 10 ASP B 42 THR B 55 1 14 HELIX 11 11 ASN B 58 GLN B 72 1 15 HELIX 12 12 GLN B 75 CYS B 93 1 19 HELIX 13 13 CYS B 93 ALA B 102 1 10 HELIX 14 14 LYS B 103 SER B 115 1 13 HELIX 15 15 THR B 124 PHE B 142 1 19 HELIX 16 16 ASP B 145 GLN B 158 1 14 SSBOND 1 CYS A 50 CYS A 89 1555 1555 2.05 SSBOND 2 CYS B 50 CYS B 89 1555 1555 2.07 CISPEP 1 ASP B 164 PRO B 165 0 -1.03 CRYST1 62.860 68.110 74.200 90.00 90.00 90.00 P 21 21 21 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 0.015908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013477 0.00000