HEADER PROTEIN TRANSPORT 23-APR-04 1VG8 TITLE GPPNHP-BOUND RAB7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-7; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: RAS-RELATED PROTEIN P23, RAS-RELATED PROTEIN BRL-RAS; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET19 KEYWDS GTP-BINDING PROTEIN, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.RAK,O.PYLYPENKO,A.NICULAE,K.PYATKOV,R.S.GOODY,K.ALEXANDROV REVDAT 4 25-OCT-23 1VG8 1 REMARK LINK REVDAT 3 04-OCT-17 1VG8 1 REMARK REVDAT 2 24-FEB-09 1VG8 1 VERSN REVDAT 1 20-JUL-04 1VG8 0 JRNL AUTH A.RAK,O.PYLYPENKO,A.NICULAE,K.PYATKOV,R.S.GOODY,K.ALEXANDROV JRNL TITL STRUCTURE OF THE RAB7:REP-1 COMPLEX: INSIGHTS INTO THE JRNL TITL 2 MECHANISM OF RAB PRENYLATION AND CHOROIDEREMIA DISEASE JRNL REF CELL(CAMBRIDGE,MASS.) V. 117 749 2004 JRNL REFN ISSN 0092-8674 JRNL PMID 15186776 JRNL DOI 10.1016/J.CELL.2004.05.017 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1233297.150 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 88795 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) : 0.198 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4440 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 13845 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 728 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5811 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 132 REMARK 3 SOLVENT ATOMS : 706 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.70 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) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.17 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.450 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.370 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.510 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 46.96 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : GNP_XPLOR_PARAM.TXT REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VG8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000006582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : PRODC REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 19.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.24000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: RAB7 FROM REP1:RAB7 COMPLEX (PDB CODE 1VG0) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 3350, 0.25M AMMONIUM REMARK 280 PHOSPHATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 1001 REMARK 465 THR A 1002 REMARK 465 SER A 1003 REMARK 465 ARG A 1004 REMARK 465 LYS A 1005 REMARK 465 LYS A 1006 REMARK 465 LYS A 1191 REMARK 465 LEU A 1192 REMARK 465 ASP A 1193 REMARK 465 LYS A 1194 REMARK 465 ASN A 1195 REMARK 465 GLU A 1196 REMARK 465 ARG A 1197 REMARK 465 ALA A 1198 REMARK 465 LYS A 1199 REMARK 465 ALA A 1200 REMARK 465 SER A 1201 REMARK 465 ALA A 1202 REMARK 465 GLU A 1203 REMARK 465 SER A 1204 REMARK 465 CYS A 1205 REMARK 465 SER A 1206 REMARK 465 CYS A 1207 REMARK 465 MET B 2001 REMARK 465 THR B 2002 REMARK 465 SER B 2003 REMARK 465 ARG B 2004 REMARK 465 LYS B 2005 REMARK 465 GLU B 2185 REMARK 465 PHE B 2186 REMARK 465 PRO B 2187 REMARK 465 GLU B 2188 REMARK 465 PRO B 2189 REMARK 465 ILE B 2190 REMARK 465 LYS B 2191 REMARK 465 LEU B 2192 REMARK 465 ASP B 2193 REMARK 465 LYS B 2194 REMARK 465 ASN B 2195 REMARK 465 GLU B 2196 REMARK 465 ARG B 2197 REMARK 465 ALA B 2198 REMARK 465 LYS B 2199 REMARK 465 ALA B 2200 REMARK 465 SER B 2201 REMARK 465 ALA B 2202 REMARK 465 GLU B 2203 REMARK 465 SER B 2204 REMARK 465 CYS B 2205 REMARK 465 SER B 2206 REMARK 465 CYS B 2207 REMARK 465 MET C 3001 REMARK 465 THR C 3002 REMARK 465 SER C 3003 REMARK 465 ARG C 3004 REMARK 465 LYS C 3005 REMARK 465 LYS C 3006 REMARK 465 GLU C 3185 REMARK 465 PHE C 3186 REMARK 465 PRO C 3187 REMARK 465 GLU C 3188 REMARK 465 PRO C 3189 REMARK 465 ILE C 3190 REMARK 465 LYS C 3191 REMARK 465 LEU C 3192 REMARK 465 ASP C 3193 REMARK 465 LYS C 3194 REMARK 465 ASN C 3195 REMARK 465 GLU C 3196 REMARK 465 ARG C 3197 REMARK 465 ALA C 3198 REMARK 465 LYS C 3199 REMARK 465 ALA C 3200 REMARK 465 SER C 3201 REMARK 465 ALA C 3202 REMARK 465 GLU C 3203 REMARK 465 SER C 3204 REMARK 465 CYS C 3205 REMARK 465 SER C 3206 REMARK 465 CYS C 3207 REMARK 465 MET D 4001 REMARK 465 THR D 4002 REMARK 465 SER D 4003 REMARK 465 ARG D 4004 REMARK 465 LYS D 4005 REMARK 465 LYS D 4006 REMARK 465 LYS D 4191 REMARK 465 LEU D 4192 REMARK 465 ASP D 4193 REMARK 465 LYS D 4194 REMARK 465 ASN D 4195 REMARK 465 GLU D 4196 REMARK 465 ARG D 4197 REMARK 465 ALA D 4198 REMARK 465 LYS D 4199 REMARK 465 ALA D 4200 REMARK 465 SER D 4201 REMARK 465 ALA D 4202 REMARK 465 GLU D 4203 REMARK 465 SER D 4204 REMARK 465 CYS D 4205 REMARK 465 SER D 4206 REMARK 465 CYS D 4207 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 ARG B2103 NE - CZ - NH1 ANGL. DEV. = 3.8 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 ASP A1054 32.80 71.60 REMARK 500 LYS A1126 35.26 73.58 REMARK 500 ASN A1131 48.08 -88.75 REMARK 500 LYS A1146 47.88 -105.93 REMARK 500 ASP B2053 51.88 38.78 REMARK 500 ASP B2054 41.39 71.20 REMARK 500 LYS B2126 34.44 76.76 REMARK 500 ASN B2131 49.12 -91.26 REMARK 500 LYS B2146 46.44 -102.71 REMARK 500 TYR B2183 -87.38 -90.32 REMARK 500 ASP C3053 60.74 36.40 REMARK 500 LYS C3126 36.38 74.83 REMARK 500 ASN C3131 51.26 -90.79 REMARK 500 LYS C3146 47.23 -101.28 REMARK 500 VAL D4075 20.36 -141.55 REMARK 500 ASP D4114 75.14 -117.31 REMARK 500 LYS D4126 35.09 73.07 REMARK 500 ASN D4131 62.65 -100.11 REMARK 500 LYS D4146 46.46 -99.26 REMARK 500 REMARK 500 REMARK: NULL 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 A1401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A1022 OG1 REMARK 620 2 THR A1040 OG1 83.8 REMARK 620 3 GNP A1400 O2G 172.9 89.7 REMARK 620 4 GNP A1400 O2B 93.2 176.8 93.4 REMARK 620 5 HOH A5002 O 89.4 87.6 93.0 91.6 REMARK 620 6 HOH A5314 O 89.4 90.6 88.1 90.2 177.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B2401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B2022 OG1 REMARK 620 2 THR B2040 OG1 84.1 REMARK 620 3 GNP B2400 O2G 174.5 90.6 REMARK 620 4 GNP B2400 O2B 92.9 176.9 92.5 REMARK 620 5 HOH B5006 O 86.9 89.7 94.5 89.8 REMARK 620 6 HOH B5315 O 91.6 90.1 87.0 90.4 178.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C3401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C3022 OG1 REMARK 620 2 THR C3040 OG1 83.7 REMARK 620 3 GNP C3400 O2G 173.6 90.2 REMARK 620 4 GNP C3400 O2B 93.9 177.5 92.1 REMARK 620 5 HOH C5001 O 87.0 90.4 95.1 90.2 REMARK 620 6 HOH C5009 O 91.3 88.4 86.4 90.9 178.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D4401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR D4022 OG1 REMARK 620 2 THR D4040 OG1 83.8 REMARK 620 3 GNP D4400 O2G 172.9 90.0 REMARK 620 4 GNP D4400 O2B 92.1 175.6 94.0 REMARK 620 5 HOH D5003 O 88.4 90.3 88.1 88.0 REMARK 620 6 HOH D5316 O 89.5 88.7 93.9 92.7 177.8 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 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 2401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 3401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 4401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP A 1400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP B 2400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP C 3400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GNP D 4400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VG0 RELATED DB: PDB REMARK 900 THE REP-1 PROTEIN IN COMPLEX WITH MONOPRENYLATED RAB7 PROTEIN REMARK 900 RELATED ID: 1VG1 RELATED DB: PDB REMARK 900 GDP-BOUND RAB7 REMARK 900 RELATED ID: 1VG9 RELATED DB: PDB REMARK 900 THE REP-1 PROTEIN IN COMPLEX WITH C-TERMINALLY TRUNCATED RAB7 REMARK 900 PROTEIN DBREF 1VG8 A 1001 1207 UNP P09527 RAB7_RAT 1 207 DBREF 1VG8 B 2001 2207 UNP P09527 RAB7_RAT 1 207 DBREF 1VG8 C 3001 3207 UNP P09527 RAB7_RAT 1 207 DBREF 1VG8 D 4001 4207 UNP P09527 RAB7_RAT 1 207 SEQRES 1 A 207 MET THR SER ARG LYS LYS VAL LEU LEU LYS VAL ILE ILE SEQRES 2 A 207 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET ASN SEQRES 3 A 207 GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR LYS ALA SEQRES 4 A 207 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL MET VAL SEQRES 5 A 207 ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP THR ALA SEQRES 6 A 207 GLY GLN GLU ARG PHE GLN SER LEU GLY VAL ALA PHE TYR SEQRES 7 A 207 ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP VAL THR SEQRES 8 A 207 ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP ARG ASP SEQRES 9 A 207 GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO GLU ASN SEQRES 10 A 207 PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP LEU GLU SEQRES 11 A 207 ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA TRP CYS SEQRES 12 A 207 TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SER ALA SEQRES 13 A 207 LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN THR ILE SEQRES 14 A 207 ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL GLU LEU SEQRES 15 A 207 TYR ASN GLU PHE PRO GLU PRO ILE LYS LEU ASP LYS ASN SEQRES 16 A 207 GLU ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS SEQRES 1 B 207 MET THR SER ARG LYS LYS VAL LEU LEU LYS VAL ILE ILE SEQRES 2 B 207 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET ASN SEQRES 3 B 207 GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR LYS ALA SEQRES 4 B 207 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL MET VAL SEQRES 5 B 207 ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP THR ALA SEQRES 6 B 207 GLY GLN GLU ARG PHE GLN SER LEU GLY VAL ALA PHE TYR SEQRES 7 B 207 ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP VAL THR SEQRES 8 B 207 ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP ARG ASP SEQRES 9 B 207 GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO GLU ASN SEQRES 10 B 207 PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP LEU GLU SEQRES 11 B 207 ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA TRP CYS SEQRES 12 B 207 TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SER ALA SEQRES 13 B 207 LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN THR ILE SEQRES 14 B 207 ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL GLU LEU SEQRES 15 B 207 TYR ASN GLU PHE PRO GLU PRO ILE LYS LEU ASP LYS ASN SEQRES 16 B 207 GLU ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS SEQRES 1 C 207 MET THR SER ARG LYS LYS VAL LEU LEU LYS VAL ILE ILE SEQRES 2 C 207 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET ASN SEQRES 3 C 207 GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR LYS ALA SEQRES 4 C 207 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL MET VAL SEQRES 5 C 207 ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP THR ALA SEQRES 6 C 207 GLY GLN GLU ARG PHE GLN SER LEU GLY VAL ALA PHE TYR SEQRES 7 C 207 ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP VAL THR SEQRES 8 C 207 ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP ARG ASP SEQRES 9 C 207 GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO GLU ASN SEQRES 10 C 207 PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP LEU GLU SEQRES 11 C 207 ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA TRP CYS SEQRES 12 C 207 TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SER ALA SEQRES 13 C 207 LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN THR ILE SEQRES 14 C 207 ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL GLU LEU SEQRES 15 C 207 TYR ASN GLU PHE PRO GLU PRO ILE LYS LEU ASP LYS ASN SEQRES 16 C 207 GLU ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS SEQRES 1 D 207 MET THR SER ARG LYS LYS VAL LEU LEU LYS VAL ILE ILE SEQRES 2 D 207 LEU GLY ASP SER GLY VAL GLY LYS THR SER LEU MET ASN SEQRES 3 D 207 GLN TYR VAL ASN LYS LYS PHE SER ASN GLN TYR LYS ALA SEQRES 4 D 207 THR ILE GLY ALA ASP PHE LEU THR LYS GLU VAL MET VAL SEQRES 5 D 207 ASP ASP ARG LEU VAL THR MET GLN ILE TRP ASP THR ALA SEQRES 6 D 207 GLY GLN GLU ARG PHE GLN SER LEU GLY VAL ALA PHE TYR SEQRES 7 D 207 ARG GLY ALA ASP CYS CYS VAL LEU VAL PHE ASP VAL THR SEQRES 8 D 207 ALA PRO ASN THR PHE LYS THR LEU ASP SER TRP ARG ASP SEQRES 9 D 207 GLU PHE LEU ILE GLN ALA SER PRO ARG ASP PRO GLU ASN SEQRES 10 D 207 PHE PRO PHE VAL VAL LEU GLY ASN LYS ILE ASP LEU GLU SEQRES 11 D 207 ASN ARG GLN VAL ALA THR LYS ARG ALA GLN ALA TRP CYS SEQRES 12 D 207 TYR SER LYS ASN ASN ILE PRO TYR PHE GLU THR SER ALA SEQRES 13 D 207 LYS GLU ALA ILE ASN VAL GLU GLN ALA PHE GLN THR ILE SEQRES 14 D 207 ALA ARG ASN ALA LEU LYS GLN GLU THR GLU VAL GLU LEU SEQRES 15 D 207 TYR ASN GLU PHE PRO GLU PRO ILE LYS LEU ASP LYS ASN SEQRES 16 D 207 GLU ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS HET MG A1401 1 HET GNP A1400 32 HET MG B2401 1 HET GNP B2400 32 HET MG C3401 1 HET GNP C3400 32 HET MG D4401 1 HET GNP D4400 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 5 MG 4(MG 2+) FORMUL 6 GNP 4(C10 H17 N6 O13 P3) FORMUL 13 HOH *706(H2 O) HELIX 1 1 GLY A 1020 LYS A 1031 1 12 HELIX 2 2 GLN A 1067 GLN A 1071 5 5 HELIX 3 3 VAL A 1075 ARG A 1079 5 5 HELIX 4 4 ALA A 1092 THR A 1098 1 7 HELIX 5 5 THR A 1098 SER A 1111 1 14 HELIX 6 6 ASP A 1114 PHE A 1118 5 5 HELIX 7 7 ALA A 1135 LYS A 1146 1 12 HELIX 8 8 ASN A 1161 PHE A 1186 1 26 HELIX 9 9 GLY B 2020 LYS B 2031 1 12 HELIX 10 10 GLN B 2067 GLN B 2071 5 5 HELIX 11 11 VAL B 2075 ARG B 2079 5 5 HELIX 12 12 ALA B 2092 THR B 2098 1 7 HELIX 13 13 THR B 2098 SER B 2111 1 14 HELIX 14 14 ASP B 2114 PHE B 2118 5 5 HELIX 15 15 ALA B 2135 LYS B 2146 1 12 HELIX 16 16 ASN B 2161 ASN B 2184 1 24 HELIX 17 17 GLY C 3020 LYS C 3031 1 12 HELIX 18 18 GLN C 3067 GLN C 3071 5 5 HELIX 19 19 VAL C 3075 ARG C 3079 5 5 HELIX 20 20 ALA C 3092 THR C 3098 1 7 HELIX 21 21 THR C 3098 SER C 3111 1 14 HELIX 22 22 ASP C 3114 PHE C 3118 5 5 HELIX 23 23 ALA C 3135 LYS C 3146 1 12 HELIX 24 24 ASN C 3161 ASN C 3184 1 24 HELIX 25 25 GLY D 4020 LYS D 4031 1 12 HELIX 26 26 GLN D 4067 GLN D 4071 5 5 HELIX 27 27 VAL D 4075 ARG D 4079 5 5 HELIX 28 28 ALA D 4092 THR D 4098 1 7 HELIX 29 29 THR D 4098 SER D 4111 1 14 HELIX 30 30 ASP D 4114 PHE D 4118 5 5 HELIX 31 31 ALA D 4135 LYS D 4146 1 12 HELIX 32 32 ASN D 4161 PHE D 4186 1 26 SHEET 1 A 6 ALA A1043 MET A1051 0 SHEET 2 A 6 LEU A1056 THR A1064 -1 O MET A1059 N LYS A1048 SHEET 3 A 6 LEU A1008 LEU A1014 1 N LEU A1009 O GLN A1060 SHEET 4 A 6 CYS A1083 ASP A1089 1 O VAL A1085 N ILE A1012 SHEET 5 A 6 PHE A1120 ASN A1125 1 O ASN A1125 N PHE A1088 SHEET 6 A 6 TYR A1151 GLU A1153 1 O PHE A1152 N VAL A1122 SHEET 1 B 6 ASP B2044 MET B2051 0 SHEET 2 B 6 LEU B2056 ASP B2063 -1 O MET B2059 N LYS B2048 SHEET 3 B 6 LEU B2008 GLY B2015 1 N VAL B2011 O TRP B2062 SHEET 4 B 6 CYS B2083 ASP B2089 1 O VAL B2085 N ILE B2012 SHEET 5 B 6 PHE B2120 ASN B2125 1 O ASN B2125 N PHE B2088 SHEET 6 B 6 TYR B2151 THR B2154 1 O THR B2154 N GLY B2124 SHEET 1 C 6 ASP C3044 VAL C3052 0 SHEET 2 C 6 ARG C3055 ASP C3063 -1 O ARG C3055 N VAL C3052 SHEET 3 C 6 LEU C3008 GLY C3015 1 N LEU C3009 O GLN C3060 SHEET 4 C 6 CYS C3083 ASP C3089 1 O VAL C3085 N ILE C3012 SHEET 5 C 6 PHE C3120 ASN C3125 1 O LEU C3123 N LEU C3086 SHEET 6 C 6 TYR C3151 GLU C3153 1 O PHE C3152 N GLY C3124 SHEET 1 D 6 ALA D4043 MET D4051 0 SHEET 2 D 6 LEU D4056 THR D4064 -1 O MET D4059 N LYS D4048 SHEET 3 D 6 LEU D4008 LEU D4014 1 N LEU D4009 O GLN D4060 SHEET 4 D 6 CYS D4083 ASP D4089 1 O VAL D4085 N ILE D4012 SHEET 5 D 6 PHE D4120 ASN D4125 1 O ASN D4125 N PHE D4088 SHEET 6 D 6 TYR D4151 THR D4154 1 O PHE D4152 N GLY D4124 LINK OG1 THR A1022 MG MG A1401 1555 1555 2.09 LINK OG1 THR A1040 MG MG A1401 1555 1555 2.08 LINK O2G GNP A1400 MG MG A1401 1555 1555 2.03 LINK O2B GNP A1400 MG MG A1401 1555 1555 1.99 LINK MG MG A1401 O HOH A5002 1555 1555 2.21 LINK MG MG A1401 O HOH A5314 1555 1555 2.10 LINK OG1 THR B2022 MG MG B2401 1555 1555 2.05 LINK OG1 THR B2040 MG MG B2401 1555 1555 2.13 LINK O2G GNP B2400 MG MG B2401 1555 1555 2.01 LINK O2B GNP B2400 MG MG B2401 1555 1555 2.07 LINK MG MG B2401 O HOH B5006 1555 1555 2.07 LINK MG MG B2401 O HOH B5315 1555 1555 2.14 LINK OG1 THR C3022 MG MG C3401 1555 1555 2.07 LINK OG1 THR C3040 MG MG C3401 1555 1555 2.18 LINK O2G GNP C3400 MG MG C3401 1555 1555 2.04 LINK O2B GNP C3400 MG MG C3401 1555 1555 2.04 LINK MG MG C3401 O HOH C5001 1555 1555 2.10 LINK MG MG C3401 O HOH C5009 1555 1555 2.18 LINK OG1 THR D4022 MG MG D4401 1555 1555 2.05 LINK OG1 THR D4040 MG MG D4401 1555 1555 2.10 LINK O2G GNP D4400 MG MG D4401 1555 1555 2.02 LINK O2B GNP D4400 MG MG D4401 1555 1555 2.01 LINK MG MG D4401 O HOH D5003 1555 1555 2.14 LINK MG MG D4401 O HOH D5316 1555 1555 2.12 SITE 1 AC1 5 THR A1022 THR A1040 GNP A1400 HOH A5002 SITE 2 AC1 5 HOH A5314 SITE 1 AC2 5 THR B2022 THR B2040 GNP B2400 HOH B5006 SITE 2 AC2 5 HOH B5315 SITE 1 AC3 5 THR C3022 THR C3040 GNP C3400 HOH C5001 SITE 2 AC3 5 HOH C5009 SITE 1 AC4 5 THR D4022 THR D4040 GNP D4400 HOH D5003 SITE 2 AC4 5 HOH D5316 SITE 1 AC5 27 SER A1017 GLY A1018 VAL A1019 GLY A1020 SITE 2 AC5 27 LYS A1021 THR A1022 SER A1023 PHE A1033 SITE 3 AC5 27 SER A1034 ASN A1035 TYR A1037 THR A1040 SITE 4 AC5 27 GLY A1066 ASN A1125 LYS A1126 ASP A1128 SITE 5 AC5 27 LEU A1129 SER A1155 ALA A1156 LYS A1157 SITE 6 AC5 27 MG A1401 HOH A5002 HOH A5017 HOH A5033 SITE 7 AC5 27 HOH A5079 HOH A5314 HOH A5456 SITE 1 AC6 26 SER B2017 GLY B2018 VAL B2019 GLY B2020 SITE 2 AC6 26 LYS B2021 THR B2022 SER B2023 PHE B2033 SITE 3 AC6 26 SER B2034 ASN B2035 TYR B2037 THR B2040 SITE 4 AC6 26 GLY B2066 ASN B2125 LYS B2126 ASP B2128 SITE 5 AC6 26 LEU B2129 SER B2155 ALA B2156 LYS B2157 SITE 6 AC6 26 MG B2401 HOH B5006 HOH B5020 HOH B5028 SITE 7 AC6 26 HOH B5156 HOH B5315 SITE 1 AC7 26 SER C3017 GLY C3018 VAL C3019 GLY C3020 SITE 2 AC7 26 LYS C3021 THR C3022 SER C3023 PHE C3033 SITE 3 AC7 26 SER C3034 ASN C3035 TYR C3037 THR C3040 SITE 4 AC7 26 GLY C3066 ASN C3125 LYS C3126 ASP C3128 SITE 5 AC7 26 LEU C3129 SER C3155 ALA C3156 LYS C3157 SITE 6 AC7 26 MG C3401 HOH C5001 HOH C5009 HOH C5013 SITE 7 AC7 26 HOH C5032 HOH C5219 SITE 1 AC8 28 SER D4017 GLY D4018 VAL D4019 GLY D4020 SITE 2 AC8 28 LYS D4021 THR D4022 SER D4023 PHE D4033 SITE 3 AC8 28 SER D4034 ASN D4035 TYR D4037 THR D4040 SITE 4 AC8 28 GLY D4066 ASN D4125 LYS D4126 ASP D4128 SITE 5 AC8 28 LEU D4129 SER D4155 ALA D4156 LYS D4157 SITE 6 AC8 28 MG D4401 HOH D5003 HOH D5024 HOH D5027 SITE 7 AC8 28 HOH D5069 HOH D5177 HOH D5316 HOH D5425 CRYST1 57.058 57.071 74.310 71.73 71.69 77.65 P 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 0.017526 -0.003838 -0.004959 0.00000 SCALE2 0.000000 0.017937 -0.004940 0.00000 SCALE3 0.000000 0.000000 0.014703 0.00000