HEADER PROTEIN BINDING/PROTEIN TRANSPORT 22-APR-04 1VG0 TITLE THE CRYSTAL STRUCTURES OF THE REP-1 PROTEIN IN COMPLEX WITH TITLE 2 MONOPRENYLATED RAB7 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB PROTEINS GERANYLGERANYLTRANSFERASE COMPONENT A 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAB ESCORT PROTEIN 1, REP-1; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAS-RELATED PROTEIN RAB-7; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: RAS-RELATED PROTEIN P23, RAS-RELATED PROTEIN BRL-RAS; COMPND 11 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: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PBLUEBAC; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: NORWAY RAT; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET19 KEYWDS RAB PRENYLATION, POST-TRANSLATIONAL MODIFICATION, PROTEIN BINDING- KEYWDS 2 PROTEIN TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.RAK,O.PYLYPENKO,A.NICULAE,K.PYATKOV,R.S.GOODY,K.ALEXANDROV REVDAT 5 25-OCT-23 1VG0 1 REMARK REVDAT 4 10-NOV-21 1VG0 1 REMARK SEQADV LINK REVDAT 3 04-OCT-17 1VG0 1 REMARK REVDAT 2 24-FEB-09 1VG0 1 VERSN REVDAT 1 20-JUL-04 1VG0 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. 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) : 18.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2781170.140 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 45306 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) : 0.188 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2265 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7146 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 376 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 438 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.00 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) : 0.23 REMARK 3 ESD FROM SIGMAA (A) : 0.19 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.27 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 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) : 2.490 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.410 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.080 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.260 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 33.79 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 : PG4_XPLOR_PARAM.TXT REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : GDP-GER-PARAM.TXT REMARK 3 PARAMETER FILE 6 : 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 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1VG0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000006574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-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) : 0.9393 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL 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 : 45399 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 18.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.1900 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) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.610 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: REP-1 FROM RABGGTASE:REP-1 COMPLEX (PDB CODE 1LTX) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 0.4M DIAMMONIUM REMARK 280 TARTRATE, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 32.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.65000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.65000 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: 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 64 REMARK 465 ASN A 65 REMARK 465 ASN A 66 REMARK 465 ASP A 67 REMARK 465 VAL A 68 REMARK 465 VAL A 69 REMARK 465 THR A 70 REMARK 465 GLU A 71 REMARK 465 ASN A 72 REMARK 465 SER A 73 REMARK 465 ASP A 107 REMARK 465 LEU A 108 REMARK 465 HIS A 109 REMARK 465 LYS A 110 REMARK 465 ASP A 111 REMARK 465 VAL A 112 REMARK 465 GLU A 113 REMARK 465 GLU A 114 REMARK 465 ALA A 115 REMARK 465 GLY A 116 REMARK 465 ALA A 117 REMARK 465 LEU A 118 REMARK 465 GLN A 119 REMARK 465 LYS A 120 REMARK 465 ASN A 121 REMARK 465 HIS A 122 REMARK 465 ALA A 123 REMARK 465 SER A 124 REMARK 465 VAL A 125 REMARK 465 THR A 126 REMARK 465 SER A 127 REMARK 465 ALA A 128 REMARK 465 GLN A 129 REMARK 465 SER A 130 REMARK 465 ALA A 131 REMARK 465 GLU A 132 REMARK 465 ALA A 133 REMARK 465 ALA A 134 REMARK 465 GLU A 135 REMARK 465 ALA A 136 REMARK 465 ALA A 137 REMARK 465 GLU A 138 REMARK 465 THR A 139 REMARK 465 SER A 140 REMARK 465 CYS A 141 REMARK 465 LEU A 142 REMARK 465 PRO A 143 REMARK 465 THR A 144 REMARK 465 ALA A 145 REMARK 465 VAL A 146 REMARK 465 GLU A 147 REMARK 465 PRO A 148 REMARK 465 LEU A 149 REMARK 465 SER A 150 REMARK 465 MET A 151 REMARK 465 GLY A 152 REMARK 465 SER A 153 REMARK 465 CYS A 154 REMARK 465 GLU A 155 REMARK 465 ILE A 156 REMARK 465 PRO A 157 REMARK 465 ALA A 158 REMARK 465 GLU A 159 REMARK 465 GLN A 160 REMARK 465 SER A 161 REMARK 465 GLN A 162 REMARK 465 CYS A 163 REMARK 465 PRO A 164 REMARK 465 GLY A 165 REMARK 465 PRO A 166 REMARK 465 GLU A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 PRO A 170 REMARK 465 GLU A 171 REMARK 465 VAL A 172 REMARK 465 ASN A 173 REMARK 465 ASP A 174 REMARK 465 ALA A 175 REMARK 465 GLU A 176 REMARK 465 ALA A 177 REMARK 465 THR A 178 REMARK 465 GLY A 179 REMARK 465 LYS A 180 REMARK 465 LYS A 181 REMARK 465 GLU A 182 REMARK 465 ASN A 183 REMARK 465 SER A 184 REMARK 465 ASP A 185 REMARK 465 ALA A 186 REMARK 465 LYS A 187 REMARK 465 SER A 188 REMARK 465 SER A 189 REMARK 465 THR A 190 REMARK 465 GLU A 191 REMARK 465 GLU A 192 REMARK 465 PRO A 193 REMARK 465 SER A 194 REMARK 465 GLU A 195 REMARK 465 ASN A 196 REMARK 465 VAL A 197 REMARK 465 PRO A 198 REMARK 465 LYS A 199 REMARK 465 VAL A 200 REMARK 465 GLN A 201 REMARK 465 ASP A 202 REMARK 465 ASN A 203 REMARK 465 THR A 204 REMARK 465 GLU A 205 REMARK 465 THR A 206 REMARK 465 PRO A 207 REMARK 465 LYS A 208 REMARK 465 LYS A 209 REMARK 465 ASN A 210 REMARK 465 THR A 341 REMARK 465 SER A 342 REMARK 465 GLU A 532 REMARK 465 ALA A 533 REMARK 465 GLU A 534 REMARK 465 ASN A 535 REMARK 465 GLU A 536 REMARK 465 GLN A 537 REMARK 465 VAL A 538 REMARK 465 ASN A 607 REMARK 465 PRO A 608 REMARK 465 GLU A 609 REMARK 465 ASP A 610 REMARK 465 ILE A 611 REMARK 465 VAL A 612 REMARK 465 LEU A 613 REMARK 465 ASP A 614 REMARK 465 GLY A 615 REMARK 465 ASP A 616 REMARK 465 SER A 617 REMARK 465 SER A 618 REMARK 465 GLN A 619 REMARK 465 GLN A 620 REMARK 465 GLU A 621 REMARK 465 VAL A 622 REMARK 465 PRO A 623 REMARK 465 GLU A 624 REMARK 465 SER A 625 REMARK 465 SER A 626 REMARK 465 VAL A 627 REMARK 465 THR A 628 REMARK 465 PRO A 629 REMARK 465 GLU A 630 REMARK 465 THR A 631 REMARK 465 ASN A 632 REMARK 465 SER A 633 REMARK 465 GLU A 634 REMARK 465 THR A 635 REMARK 465 PRO A 636 REMARK 465 LYS A 637 REMARK 465 GLU A 638 REMARK 465 SER A 639 REMARK 465 THR A 640 REMARK 465 VAL A 641 REMARK 465 LEU A 642 REMARK 465 GLY A 643 REMARK 465 ASN A 644 REMARK 465 PRO A 645 REMARK 465 GLU A 646 REMARK 465 GLU A 647 REMARK 465 PRO A 648 REMARK 465 SER A 649 REMARK 465 GLU A 650 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 ARG B 4 REMARK 465 LYS B 5 REMARK 465 GLN B 36 REMARK 465 TYR B 37 REMARK 465 LYS B 38 REMARK 465 ALA B 39 REMARK 465 THR B 40 REMARK 465 ASP B 193 REMARK 465 LYS B 194 REMARK 465 ASN B 195 REMARK 465 GLU B 196 REMARK 465 ARG B 197 REMARK 465 ALA B 198 REMARK 465 LYS B 199 REMARK 465 ALA B 200 REMARK 465 SER B 201 REMARK 465 ALA B 202 REMARK 465 GLU B 203 REMARK 465 SER B 204 REMARK 465 CYS B 205 REMARK 465 SER B 206 REMARK 465 CYS B 207 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 A 76 CG CD OE1 NE2 REMARK 470 ARG A 211 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 498 CG CD CE NZ REMARK 470 ILE A 531 CG1 CG2 CD1 REMARK 470 GLU A 539 CG CD OE1 OE2 REMARK 470 LYS B 6 CG CD CE NZ REMARK 470 ILE B 41 CG1 CG2 CD1 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 GLN A 76 -38.77 -39.57 REMARK 500 ARG A 264 77.87 -119.34 REMARK 500 GLU A 265 58.25 72.40 REMARK 500 GLU A 303 3.38 -64.28 REMARK 500 ILE A 338 -62.88 -101.39 REMARK 500 TYR A 375 -4.64 83.20 REMARK 500 GLU A 409 -70.91 -77.26 REMARK 500 LYS A 511 -141.09 -124.38 REMARK 500 ASP B 44 -82.57 -141.04 REMARK 500 SER B 111 62.87 39.87 REMARK 500 GLU B 116 -16.62 -48.49 REMARK 500 LYS B 146 53.35 -119.51 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 B3000 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 22 OG1 REMARK 620 2 GDP B1557 O3B 89.5 REMARK 620 3 HOH B5583 O 89.1 105.5 REMARK 620 4 HOH B5584 O 92.1 160.5 94.0 REMARK 620 5 HOH B5585 O 170.5 82.5 98.0 93.7 REMARK 620 6 HOH B5586 O 83.7 74.8 172.8 86.0 89.2 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 B 3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GER A 952 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 1557 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 B 5502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LTX RELATED DB: PDB REMARK 900 RABGGTASE:REP1 COMPLEX STRUCTURE REMARK 900 RELATED ID: 1VG1 RELATED DB: PDB REMARK 900 GDP-BOUND RAB7 REMARK 900 RELATED ID: 1VG8 RELATED DB: PDB REMARK 900 GPPNHP-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 1VG0 A 1 650 UNP P37727 RAE1_RAT 1 650 DBREF 1VG0 B 1 207 UNP P09527 RAB7_RAT 1 207 SEQADV 1VG0 LYS A 231 UNP P37727 GLN 231 ENGINEERED MUTATION SEQADV 1VG0 ARG A 462 UNP P37727 LYS 462 ENGINEERED MUTATION SEQADV 1VG0 THR A 473 UNP P37727 ALA 473 ENGINEERED MUTATION SEQADV 1VG0 ALA A 483 UNP P37727 GLY 483 ENGINEERED MUTATION SEQRES 1 A 650 MET ALA ASP ASN LEU PRO SER ASP PHE ASP VAL ILE VAL SEQRES 2 A 650 ILE GLY THR GLY LEU PRO GLU SER ILE ILE ALA ALA ALA SEQRES 3 A 650 CYS SER ARG SER GLY GLN ARG VAL LEU HIS VAL ASP SER SEQRES 4 A 650 ARG SER TYR TYR GLY GLY ASN TRP ALA SER PHE SER PHE SEQRES 5 A 650 SER GLY LEU LEU SER TRP LEU LYS GLU TYR GLN GLU ASN SEQRES 6 A 650 ASN ASP VAL VAL THR GLU ASN SER MET TRP GLN GLU GLN SEQRES 7 A 650 ILE LEU GLU ASN GLU GLU ALA ILE PRO LEU SER SER LYS SEQRES 8 A 650 ASP LYS THR ILE GLN HIS VAL GLU VAL PHE CYS TYR ALA SEQRES 9 A 650 SER GLN ASP LEU HIS LYS ASP VAL GLU GLU ALA GLY ALA SEQRES 10 A 650 LEU GLN LYS ASN HIS ALA SER VAL THR SER ALA GLN SER SEQRES 11 A 650 ALA GLU ALA ALA GLU ALA ALA GLU THR SER CYS LEU PRO SEQRES 12 A 650 THR ALA VAL GLU PRO LEU SER MET GLY SER CYS GLU ILE SEQRES 13 A 650 PRO ALA GLU GLN SER GLN CYS PRO GLY PRO GLU SER SER SEQRES 14 A 650 PRO GLU VAL ASN ASP ALA GLU ALA THR GLY LYS LYS GLU SEQRES 15 A 650 ASN SER ASP ALA LYS SER SER THR GLU GLU PRO SER GLU SEQRES 16 A 650 ASN VAL PRO LYS VAL GLN ASP ASN THR GLU THR PRO LYS SEQRES 17 A 650 LYS ASN ARG ILE THR TYR SER GLN ILE ILE LYS GLU GLY SEQRES 18 A 650 ARG ARG PHE ASN ILE ASP LEU VAL SER LYS LEU LEU TYR SEQRES 19 A 650 SER ARG GLY LEU LEU ILE ASP LEU LEU ILE LYS SER ASN SEQRES 20 A 650 VAL SER ARG TYR ALA GLU PHE LYS ASN ILE THR ARG ILE SEQRES 21 A 650 LEU ALA PHE ARG GLU GLY THR VAL GLU GLN VAL PRO CYS SEQRES 22 A 650 SER ARG ALA ASP VAL PHE ASN SER LYS GLN LEU THR MET SEQRES 23 A 650 VAL GLU LYS ARG MET LEU MET LYS PHE LEU THR PHE CYS SEQRES 24 A 650 VAL GLU TYR GLU GLU HIS PRO ASP GLU TYR ARG ALA TYR SEQRES 25 A 650 GLU GLY THR THR PHE SER GLU TYR LEU LYS THR GLN LYS SEQRES 26 A 650 LEU THR PRO ASN LEU GLN TYR PHE VAL LEU HIS SER ILE SEQRES 27 A 650 ALA MET THR SER GLU THR THR SER CYS THR VAL ASP GLY SEQRES 28 A 650 LEU LYS ALA THR LYS LYS PHE LEU GLN CYS LEU GLY ARG SEQRES 29 A 650 TYR GLY ASN THR PRO PHE LEU PHE PRO LEU TYR GLY GLN SEQRES 30 A 650 GLY GLU LEU PRO GLN CYS PHE CYS ARG MET CYS ALA VAL SEQRES 31 A 650 PHE GLY GLY ILE TYR CYS LEU ARG HIS SER VAL GLN CYS SEQRES 32 A 650 LEU VAL VAL ASP LYS GLU SER ARG LYS CYS LYS ALA VAL SEQRES 33 A 650 ILE ASP GLN PHE GLY GLN ARG ILE ILE SER LYS HIS PHE SEQRES 34 A 650 ILE ILE GLU ASP SER TYR LEU SER GLU ASN THR CYS SER SEQRES 35 A 650 ARG VAL GLN TYR ARG GLN ILE SER ARG ALA VAL LEU ILE SEQRES 36 A 650 THR ASP GLY SER VAL LEU ARG THR ASP ALA ASP GLN GLN SEQRES 37 A 650 VAL SER ILE LEU THR VAL PRO ALA GLU GLU PRO GLY SER SEQRES 38 A 650 PHE ALA VAL ARG VAL ILE GLU LEU CYS SER SER THR MET SEQRES 39 A 650 THR CYS MET LYS GLY THR TYR LEU VAL HIS LEU THR CYS SEQRES 40 A 650 MET SER SER LYS THR ALA ARG GLU ASP LEU GLU ARG VAL SEQRES 41 A 650 VAL GLN LYS LEU PHE THR PRO TYR THR GLU ILE GLU ALA SEQRES 42 A 650 GLU ASN GLU GLN VAL GLU LYS PRO ARG LEU LEU TRP ALA SEQRES 43 A 650 LEU TYR PHE ASN MET ARG ASP SER SER ASP ILE SER ARG SEQRES 44 A 650 ASP CYS TYR ASN ASP LEU PRO SER ASN VAL TYR VAL CYS SEQRES 45 A 650 SER GLY PRO ASP SER GLY LEU GLY ASN ASP ASN ALA VAL SEQRES 46 A 650 LYS GLN ALA GLU THR LEU PHE GLN GLN ILE CYS PRO ASN SEQRES 47 A 650 GLU ASP PHE CYS PRO ALA PRO PRO ASN PRO GLU ASP ILE SEQRES 48 A 650 VAL LEU ASP GLY ASP SER SER GLN GLN GLU VAL PRO GLU SEQRES 49 A 650 SER SER VAL THR PRO GLU THR ASN SER GLU THR PRO LYS SEQRES 50 A 650 GLU SER THR VAL LEU GLY ASN PRO GLU GLU PRO SER GLU 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 HET CL A3001 1 HET GER A 952 20 HET MG B3000 1 HET GDP B1557 28 HET PG4 B5502 13 HETNAM CL CHLORIDE ION HETNAM GER GERAN-8-YL GERAN HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 3 CL CL 1- FORMUL 4 GER C20 H34 FORMUL 5 MG MG 2+ FORMUL 6 GDP C10 H15 N5 O11 P2 FORMUL 7 PG4 C8 H18 O5 FORMUL 8 HOH *438(H2 O) HELIX 1 1 GLY A 17 SER A 30 1 14 HELIX 2 2 GLY A 44 TRP A 47 5 4 HELIX 3 3 SER A 51 TYR A 62 1 12 HELIX 4 4 GLN A 63 GLN A 63 5 1 HELIX 5 5 MET A 74 ILE A 79 5 6 HELIX 6 6 THR A 213 GLU A 220 1 8 HELIX 7 7 GLY A 221 PHE A 224 5 4 HELIX 8 8 GLY A 237 ASN A 247 1 11 HELIX 9 9 VAL A 248 ALA A 252 5 5 HELIX 10 10 SER A 274 SER A 281 1 8 HELIX 11 11 THR A 285 GLU A 301 1 17 HELIX 12 12 TYR A 302 GLU A 304 5 3 HELIX 13 13 HIS A 305 ALA A 311 1 7 HELIX 14 14 THR A 316 LYS A 322 1 7 HELIX 15 15 THR A 327 ILE A 338 1 12 HELIX 16 16 CYS A 347 LEU A 362 1 16 HELIX 17 17 GLY A 378 PHE A 391 1 14 HELIX 18 18 SER A 434 LEU A 436 5 3 HELIX 19 19 CYS A 490 MET A 494 5 5 HELIX 20 20 THR A 512 PHE A 525 1 14 HELIX 21 21 SER A 558 TYR A 562 5 5 HELIX 22 22 ASN A 581 CYS A 596 1 16 HELIX 23 23 GLY B 20 LYS B 31 1 12 HELIX 24 24 GLY B 74 ARG B 79 1 6 HELIX 25 25 ALA B 92 THR B 98 1 7 HELIX 26 26 THR B 98 SER B 111 1 14 HELIX 27 27 ASP B 114 PHE B 118 5 5 HELIX 28 28 ALA B 135 SER B 145 1 11 HELIX 29 29 ASN B 161 ASN B 184 1 24 SHEET 1 A 5 ILE A 394 CYS A 396 0 SHEET 2 A 5 VAL A 34 VAL A 37 1 N HIS A 36 O ILE A 394 SHEET 3 A 5 VAL A 11 ILE A 14 1 N VAL A 13 O LEU A 35 SHEET 4 A 5 HIS A 428 GLU A 432 1 O ILE A 430 N ILE A 14 SHEET 5 A 5 VAL A 569 CYS A 572 1 O TYR A 570 N ILE A 431 SHEET 1 B 2 SER A 49 PHE A 50 0 SHEET 2 B 2 ILE A 226 ASP A 227 -1 O ILE A 226 N PHE A 50 SHEET 1 C 4 GLU A 83 PRO A 87 0 SHEET 2 C 4 VAL A 401 ASP A 407 -1 O VAL A 406 N GLU A 84 SHEET 3 C 4 CYS A 413 ASP A 418 -1 O LYS A 414 N VAL A 405 SHEET 4 C 4 ARG A 423 ILE A 425 -1 O ILE A 424 N VAL A 416 SHEET 1 D 8 ILE A 95 CYS A 102 0 SHEET 2 D 8 LEU A 543 ASP A 553 -1 O ALA A 546 N PHE A 101 SHEET 3 D 8 ARG A 447 THR A 456 -1 N ARG A 451 O PHE A 549 SHEET 4 D 8 TYR A 501 MET A 508 -1 O CYS A 507 N SER A 450 SHEET 5 D 8 VAL A 484 LEU A 489 -1 N ILE A 487 O HIS A 504 SHEET 6 D 8 SER A 470 VAL A 474 -1 N VAL A 474 O VAL A 484 SHEET 7 D 8 ARG A 259 PHE A 263 1 N LEU A 261 O ILE A 471 SHEET 8 D 8 VAL A 268 GLN A 270 -1 O GLU A 269 N ALA A 262 SHEET 1 E 3 LEU A 233 TYR A 234 0 SHEET 2 E 3 PHE A 370 PRO A 373 -1 O LEU A 371 N LEU A 233 SHEET 3 E 3 PHE A 254 ASN A 256 -1 N LYS A 255 O PHE A 372 SHEET 1 F 6 PHE B 45 VAL B 52 0 SHEET 2 F 6 ARG B 55 TRP B 62 -1 O VAL B 57 N VAL B 50 SHEET 3 F 6 LEU B 8 LEU B 14 1 N VAL B 11 O GLN B 60 SHEET 4 F 6 CYS B 83 ASP B 89 1 O VAL B 85 N LEU B 14 SHEET 5 F 6 PHE B 120 ASN B 125 1 O LEU B 123 N LEU B 86 SHEET 6 F 6 TYR B 151 THR B 154 1 O THR B 154 N GLY B 124 LINK OG1 THR B 22 MG MG B3000 1555 1555 1.92 LINK O3B GDP B1557 MG MG B3000 1555 1555 2.14 LINK MG MG B3000 O HOH B5583 1555 1555 2.07 LINK MG MG B3000 O HOH B5584 1555 1555 1.98 LINK MG MG B3000 O HOH B5585 1555 1555 1.97 LINK MG MG B3000 O HOH B5586 1555 1555 2.25 SITE 1 AC1 6 THR B 22 GDP B1557 HOH B5583 HOH B5584 SITE 2 AC1 6 HOH B5585 HOH B5586 SITE 1 AC2 4 TYR A 234 ASN A 581 HOH A3012 HOH A3026 SITE 1 AC3 8 PRO A 272 SER A 274 ARG A 275 LEU A 292 SITE 2 AC3 8 MET A 293 VAL A 300 PHE A 333 LEU A 362 SITE 1 AC4 23 ASP B 16 SER B 17 GLY B 18 VAL B 19 SITE 2 AC4 23 GLY B 20 LYS B 21 THR B 22 SER B 23 SITE 3 AC4 23 PHE B 33 ASN B 125 LYS B 126 ASP B 128 SITE 4 AC4 23 LEU B 129 SER B 155 ALA B 156 LYS B 157 SITE 5 AC4 23 MG B3000 HOH B5527 HOH B5547 HOH B5570 SITE 6 AC4 23 HOH B5583 HOH B5585 HOH B5586 SITE 1 AC5 4 GLN B 71 SER B 101 TRP B 102 GLU B 105 CRYST1 64.300 105.300 132.600 90.00 90.00 90.00 P 21 21 2 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 0.015552 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009497 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007541 0.00000