HEADER HYDROLASE 16-NOV-98 3RAB TITLE GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (RAB3A); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GTPASE DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21/DE3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS G PROTEIN, VESICULAR TRAFFICKING, GTP HYDROLYSIS, RAB PROTEIN, KEYWDS 2 NEUROTRANSMITTER RELEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.DUMAS,Z.ZHU,J.L.CONNOLLY,D.G.LAMBRIGHT REVDAT 4 13-SEP-23 3RAB 1 REMARK LINK REVDAT 3 24-FEB-09 3RAB 1 VERSN REVDAT 2 30-AUG-02 3RAB 1 SOURCE REMARK HETNAM HELIX REVDAT 2 2 1 MASTER REVDAT 1 16-APR-99 3RAB 0 JRNL AUTH J.J.DUMAS,Z.ZHU,J.L.CONNOLLY,D.G.LAMBRIGHT JRNL TITL STRUCTURAL BASIS OF ACTIVATION AND GTP HYDROLYSIS IN RAB JRNL TITL 2 PROTEINS. JRNL REF STRUCTURE FOLD.DES. V. 7 413 1999 JRNL REFN ISSN 0969-2126 JRNL PMID 10196122 JRNL DOI 10.1016/S0969-2126(99)80054-9 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 0.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 10595 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 SET) : 0.191 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1364 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 123 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.00 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.200 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3RAB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : DEC-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10595 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.19700 REMARK 200 FOR SHELL : 6.300 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: 5P21 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION CONDITIONS: 14%PEG REMARK 280 -8000,50 MM NAMES, PH 6.5, 200 MM NACL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.45000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 17.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.45000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 17.50000 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 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 ASN A 18 CG OD1 ND2 REMARK 470 ASN A 67 CG OD1 ND2 REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 ASN A 127 CG OD1 ND2 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 CYS A 184 SG 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 36 OG1 REMARK 620 2 THR A 54 OG1 81.2 REMARK 620 3 GNP A 200 O2G 166.8 89.8 REMARK 620 4 GNP A 200 O2B 91.0 172.1 98.1 REMARK 620 5 HOH A 301 O 95.3 94.3 94.9 85.3 REMARK 620 6 HOH A 318 O 87.6 91.9 83.1 88.8 173.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 200 DBREF 3RAB A 18 186 UNP P63012 RAB3A_RAT 18 186 SEQRES 1 A 169 ASN PHE ASP TYR MET PHE LYS ILE LEU ILE ILE GLY ASN SEQRES 2 A 169 SER SER VAL GLY LYS THR SER PHE LEU PHE ARG TYR ALA SEQRES 3 A 169 ASP ASP SER PHE THR PRO ALA PHE VAL SER THR VAL GLY SEQRES 4 A 169 ILE ASP PHE LYS VAL LYS THR ILE TYR ARG ASN ASP LYS SEQRES 5 A 169 ARG ILE LYS LEU GLN ILE TRP ASP THR ALA GLY GLN GLU SEQRES 6 A 169 ARG TYR ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA SEQRES 7 A 169 MET GLY PHE ILE LEU MET TYR ASP ILE THR ASN GLU GLU SEQRES 8 A 169 SER PHE ASN ALA VAL GLN ASP TRP SER THR GLN ILE LYS SEQRES 9 A 169 THR TYR SER TRP ASP ASN ALA GLN VAL LEU LEU VAL GLY SEQRES 10 A 169 ASN LYS CYS ASP MET GLU ASP GLU ARG VAL VAL SER SER SEQRES 11 A 169 GLU ARG GLY ARG GLN LEU ALA ASP HIS LEU GLY PHE GLU SEQRES 12 A 169 PHE PHE GLU ALA SER ALA LYS ASP ASN ILE ASN VAL LYS SEQRES 13 A 169 GLN THR PHE GLU ARG LEU VAL ASP VAL ILE CYS GLU LYS HET MG A 201 1 HET GNP A 200 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 2 MG MG 2+ FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 HOH *123(H2 O) HELIX 1 1 LYS A 35 ASP A 44 1 10 HELIX 2 2 GLU A 82 TYR A 91 1 10 HELIX 3 3 GLU A 107 ASN A 111 1 5 HELIX 4 4 VAL A 113 TYR A 123 1 11 HELIX 5 5 SER A 147 LEU A 157 1 11 HELIX 6 6 VAL A 172 CYS A 184 1 13 SHEET 1 A 6 GLU A 160 GLU A 163 0 SHEET 2 A 6 GLN A 129 ASN A 135 1 N LEU A 132 O GLU A 160 SHEET 3 A 6 GLY A 97 ASP A 103 1 N PHE A 98 O GLN A 129 SHEET 4 A 6 TYR A 21 GLY A 29 1 N LEU A 26 O GLY A 97 SHEET 5 A 6 LYS A 69 THR A 78 1 N LYS A 72 O TYR A 21 SHEET 6 A 6 ILE A 57 ARG A 66 -1 N ARG A 66 O LYS A 69 LINK OG1 THR A 36 MG MG A 201 1555 1555 2.25 LINK OG1 THR A 54 MG MG A 201 1555 1555 2.27 LINK O2G GNP A 200 MG MG A 201 1555 1555 2.25 LINK O2B GNP A 200 MG MG A 201 1555 1555 2.26 LINK MG MG A 201 O HOH A 301 1555 1555 2.33 LINK MG MG A 201 O HOH A 318 1555 1555 2.40 SITE 1 AC1 5 THR A 36 THR A 54 GNP A 200 HOH A 301 SITE 2 AC1 5 HOH A 318 SITE 1 AC2 26 SER A 31 SER A 32 VAL A 33 GLY A 34 SITE 2 AC2 26 LYS A 35 THR A 36 SER A 37 PHE A 47 SITE 3 AC2 26 THR A 48 PRO A 49 ALA A 50 PHE A 51 SITE 4 AC2 26 SER A 53 THR A 54 GLY A 80 ASN A 135 SITE 5 AC2 26 LYS A 136 ASP A 138 MET A 139 SER A 165 SITE 6 AC2 26 ALA A 166 LYS A 167 MG A 201 HOH A 302 SITE 7 AC2 26 HOH A 318 HOH A 566 CRYST1 88.900 35.000 58.600 90.00 107.20 90.00 C 1 2 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 0.011248 0.000000 0.003482 0.00000 SCALE2 0.000000 0.028571 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017864 0.00000