PDB Short entry for 6IYB HEADER TRANSPORT PROTEIN 14-DEC-18 6IYB TITLE STRUCTURE OF HUMAN ORP1 ANK - RAB7 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-7A; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: UNP RESIDUES 2-195; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: OXYSTEROL-BINDING PROTEIN-RELATED PROTEIN 1; COMPND 9 CHAIN: B, D; COMPND 10 FRAGMENT: UNP RESIDUES 5-152; COMPND 11 SYNONYM: OSBP-RELATED PROTEIN 1; COMPND 12 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: RAB7A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: OSBPL1A; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PHIS2-THR KEYWDS OXYSTEROL-BINDING PROTEIN, ORP1, MEMBRANE CONTACT SITE, RAB7, ANKYRIN KEYWDS 2 REPEAT, CHOLESTEROL, RILP, LATE ENDOSOME, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.TONG,Y.J.IM REVDAT 2 22-NOV-23 6IYB 1 LINK REVDAT 1 13-MAR-19 6IYB 0 JRNL AUTH J.TONG,L.TAN,C.CHUN,Y.J.IM JRNL TITL STRUCTURAL BASIS OF HUMAN ORP1-RAB7 INTERACTION FOR THE JRNL TITL 2 LATE-ENDOSOME AND LYSOSOME TARGETING. JRNL REF PLOS ONE V. 14 11724 2019 JRNL REFN ESSN 1932-6203 JRNL PMID 30721249 JRNL DOI 10.1371/JOURNAL.PONE.0211724 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49988 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 2545 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 26.2877 - 5.4657 0.90 2602 137 0.1874 0.2130 REMARK 3 2 5.4657 - 4.3446 0.99 2730 145 0.1600 0.1694 REMARK 3 3 4.3446 - 3.7973 0.99 2716 142 0.1571 0.2083 REMARK 3 4 3.7973 - 3.4509 1.00 2646 154 0.1739 0.2204 REMARK 3 5 3.4509 - 3.2040 1.00 2706 147 0.1971 0.2415 REMARK 3 6 3.2040 - 3.0154 1.00 2673 131 0.2112 0.2323 REMARK 3 7 3.0154 - 2.8646 1.00 2675 142 0.2120 0.2578 REMARK 3 8 2.8646 - 2.7400 1.00 2641 147 0.2205 0.2829 REMARK 3 9 2.7400 - 2.6346 1.00 2649 144 0.2267 0.2542 REMARK 3 10 2.6346 - 2.5438 1.00 2678 135 0.2160 0.2529 REMARK 3 11 2.5438 - 2.4643 1.00 2660 136 0.2217 0.2675 REMARK 3 12 2.4643 - 2.3939 1.00 2599 165 0.2236 0.2463 REMARK 3 13 2.3939 - 2.3310 1.00 2655 148 0.2242 0.2722 REMARK 3 14 2.3310 - 2.2741 1.00 2639 138 0.2187 0.2846 REMARK 3 15 2.2741 - 2.2224 1.00 2620 157 0.2257 0.2681 REMARK 3 16 2.2224 - 2.1752 1.00 2648 130 0.2246 0.2498 REMARK 3 17 2.1752 - 2.1317 1.00 2638 131 0.2153 0.2663 REMARK 3 18 2.1317 - 2.0915 0.86 2268 116 0.2389 0.2724 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.30 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 4971 REMARK 3 ANGLE : 0.926 6739 REMARK 3 CHIRALITY : 0.053 761 REMARK 3 PLANARITY : 0.005 869 REMARK 3 DIHEDRAL : 20.982 2991 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6IYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1300010156. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50042 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 39.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1T91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA3CITRATE-HCL, 1 M LICL, 20% REMARK 280 PEG 1000, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 27.56800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.23800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.61100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.23800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.56800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.61100 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 GLY A -4 REMARK 465 SER A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 ARG A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 179 REMARK 465 VAL A 180 REMARK 465 GLU A 181 REMARK 465 LEU A 182 REMARK 465 TYR A 183 REMARK 465 ASN A 184 REMARK 465 GLU A 185 REMARK 465 PHE A 186 REMARK 465 PRO A 187 REMARK 465 GLU A 188 REMARK 465 PRO A 189 REMARK 465 ILE A 190 REMARK 465 LYS A 191 REMARK 465 LEU A 192 REMARK 465 ASP A 193 REMARK 465 LYS A 194 REMARK 465 ASN A 195 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 ALA B 1 REMARK 465 MET B 2 REMARK 465 GLY B 3 REMARK 465 ARG B 139 REMARK 465 LYS B 140 REMARK 465 LEU B 141 REMARK 465 GLU B 142 REMARK 465 GLU B 143 REMARK 465 LEU B 144 REMARK 465 LEU B 145 REMARK 465 LEU B 146 REMARK 465 ALA B 147 REMARK 465 ALA B 148 REMARK 465 ALA B 149 REMARK 465 ARG B 150 REMARK 465 GLU B 151 REMARK 465 GLY B 152 REMARK 465 GLY C -4 REMARK 465 SER C -3 REMARK 465 ALA C -2 REMARK 465 MET C -1 REMARK 465 GLY C 0 REMARK 465 SER C 1 REMARK 465 THR C 2 REMARK 465 SER C 3 REMARK 465 ARG C 4 REMARK 465 LYS C 5 REMARK 465 LYS C 6 REMARK 465 GLU C 179 REMARK 465 VAL C 180 REMARK 465 GLU C 181 REMARK 465 LEU C 182 REMARK 465 TYR C 183 REMARK 465 ASN C 184 REMARK 465 GLU C 185 REMARK 465 PHE C 186 REMARK 465 PRO C 187 REMARK 465 GLU C 188 REMARK 465 PRO C 189 REMARK 465 ILE C 190 REMARK 465 LYS C 191 REMARK 465 LEU C 192 REMARK 465 ASP C 193 REMARK 465 LYS C 194 REMARK 465 ASN C 195 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 ALA D 1 REMARK 465 MET D 2 REMARK 465 GLN D 138 REMARK 465 ARG D 139 REMARK 465 LYS D 140 REMARK 465 LEU D 141 REMARK 465 GLU D 142 REMARK 465 GLU D 143 REMARK 465 LEU D 144 REMARK 465 LEU D 145 REMARK 465 LEU D 146 REMARK 465 ALA D 147 REMARK 465 ALA D 148 REMARK 465 ALA D 149 REMARK 465 ARG D 150 REMARK 465 GLU D 151 REMARK 465 GLY D 152 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 78 O HOH A 1401 2.03 REMARK 500 O HOH A 1413 O HOH A 1532 2.06 REMARK 500 OE2 GLU A 105 O HOH A 1401 2.10 REMARK 500 O HOH A 1464 O HOH A 1535 2.11 REMARK 500 OE2 GLU A 49 O HOH A 1402 2.11 REMARK 500 NZ LYS B 94 O HOH B 201 2.12 REMARK 500 O HOH B 241 O HOH B 245 2.14 REMARK 500 N SER B 4 O HOH B 202 2.16 REMARK 500 O HOH B 202 O HOH B 250 2.16 REMARK 500 O HOH A 1478 O HOH A 1519 2.16 REMARK 500 NH1 ARG B 30 OE2 GLU B 32 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1551 O HOH A 1553 4445 2.04 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 A 53 -110.47 52.17 REMARK 500 SER A 72 -147.19 -111.71 REMARK 500 LYS A 126 33.19 76.99 REMARK 500 ASN A 131 37.68 71.58 REMARK 500 LYS A 146 48.01 -99.87 REMARK 500 ASN B 46 25.66 -162.63 REMARK 500 SER C 72 -136.35 -118.48 REMARK 500 LYS C 126 35.42 73.24 REMARK 500 GLU C 130 -73.42 -63.80 REMARK 500 LYS C 146 41.62 -106.20 REMARK 500 ASN D 46 22.50 -154.53 REMARK 500 ASN D 78 -169.35 -102.19 REMARK 500 ASN D 104 37.36 72.72 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 A1301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 81.1 REMARK 620 3 GTP A1302 O3G 169.1 89.8 REMARK 620 4 GTP A1302 O2B 91.5 166.8 96.2 REMARK 620 5 HOH A1425 O 90.1 98.0 97.3 92.8 REMARK 620 6 HOH A1431 O 81.1 81.7 91.7 86.4 171.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C1301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C 22 OG1 REMARK 620 2 THR C 40 OG1 83.1 REMARK 620 3 GTP C1302 O3G 167.4 85.8 REMARK 620 4 GTP C1302 O1B 96.5 179.6 94.6 REMARK 620 5 HOH C1403 O 91.5 95.2 83.7 84.7 REMARK 620 6 HOH C1407 O 89.7 80.0 94.2 100.1 174.9 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 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP A 1302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 1301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GTP C 1302 DBREF 6IYB A 2 195 UNP P51149 RAB7A_HUMAN 2 195 DBREF 6IYB B 5 152 UNP Q9BXW6 OSBL1_HUMAN 5 152 DBREF 6IYB C 2 195 UNP P51149 RAB7A_HUMAN 2 195 DBREF 6IYB D 5 152 UNP Q9BXW6 OSBL1_HUMAN 5 152 SEQADV 6IYB GLY A -4 UNP P51149 EXPRESSION TAG SEQADV 6IYB SER A -3 UNP P51149 EXPRESSION TAG SEQADV 6IYB ALA A -2 UNP P51149 EXPRESSION TAG SEQADV 6IYB MET A -1 UNP P51149 EXPRESSION TAG SEQADV 6IYB GLY A 0 UNP P51149 EXPRESSION TAG SEQADV 6IYB SER A 1 UNP P51149 EXPRESSION TAG SEQADV 6IYB LEU A 67 UNP P51149 GLN 67 ENGINEERED MUTATION SEQADV 6IYB A UNP P51149 LEU 73 DELETION SEQADV 6IYB GLY B -1 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB SER B 0 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB ALA B 1 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB MET B 2 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB GLY B 3 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB SER B 4 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB GLY C -4 UNP P51149 EXPRESSION TAG SEQADV 6IYB SER C -3 UNP P51149 EXPRESSION TAG SEQADV 6IYB ALA C -2 UNP P51149 EXPRESSION TAG SEQADV 6IYB MET C -1 UNP P51149 EXPRESSION TAG SEQADV 6IYB GLY C 0 UNP P51149 EXPRESSION TAG SEQADV 6IYB SER C 1 UNP P51149 EXPRESSION TAG SEQADV 6IYB LEU C 67 UNP P51149 GLN 67 ENGINEERED MUTATION SEQADV 6IYB C UNP P51149 LEU 73 DELETION SEQADV 6IYB GLY D -1 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB SER D 0 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB ALA D 1 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB MET D 2 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB GLY D 3 UNP Q9BXW6 EXPRESSION TAG SEQADV 6IYB SER D 4 UNP Q9BXW6 EXPRESSION TAG SEQRES 1 A 199 GLY SER ALA MET GLY SER THR SER ARG LYS LYS VAL LEU SEQRES 2 A 199 LEU LYS VAL ILE ILE LEU GLY ASP SER GLY VAL GLY LYS SEQRES 3 A 199 THR SER LEU MET ASN GLN TYR VAL ASN LYS LYS PHE SER SEQRES 4 A 199 ASN GLN TYR LYS ALA THR ILE GLY ALA ASP PHE LEU THR SEQRES 5 A 199 LYS GLU VAL MET VAL ASP ASP ARG LEU VAL THR MET GLN SEQRES 6 A 199 ILE TRP ASP THR ALA GLY LEU GLU ARG PHE GLN SER GLY SEQRES 7 A 199 VAL ALA PHE TYR ARG GLY ALA ASP CYS CYS VAL LEU VAL SEQRES 8 A 199 PHE ASP VAL THR ALA PRO ASN THR PHE LYS THR LEU ASP SEQRES 9 A 199 SER TRP ARG ASP GLU PHE LEU ILE GLN ALA SER PRO ARG SEQRES 10 A 199 ASP PRO GLU ASN PHE PRO PHE VAL VAL LEU GLY ASN LYS SEQRES 11 A 199 ILE ASP LEU GLU ASN ARG GLN VAL ALA THR LYS ARG ALA SEQRES 12 A 199 GLN ALA TRP CYS TYR SER LYS ASN ASN ILE PRO TYR PHE SEQRES 13 A 199 GLU THR SER ALA LYS GLU ALA ILE ASN VAL GLU GLN ALA SEQRES 14 A 199 PHE GLN THR ILE ALA ARG ASN ALA LEU LYS GLN GLU THR SEQRES 15 A 199 GLU VAL GLU LEU TYR ASN GLU PHE PRO GLU PRO ILE LYS SEQRES 16 A 199 LEU ASP LYS ASN SEQRES 1 B 154 GLY SER ALA MET GLY SER ALA GLU GLN GLN LEU LEU HIS SEQRES 2 B 154 HIS ALA ARG ASN GLY ASN ALA GLU GLU VAL ARG GLN LEU SEQRES 3 B 154 LEU GLU THR MET ALA ARG ASN GLU VAL ILE ALA ASP ILE SEQRES 4 B 154 ASN CYS LYS GLY ARG SER LYS SER ASN LEU GLY TRP THR SEQRES 5 B 154 PRO LEU HIS LEU ALA CYS TYR PHE GLY HIS ARG GLN VAL SEQRES 6 B 154 VAL GLN ASP LEU LEU LYS ALA GLY ALA GLU VAL ASN VAL SEQRES 7 B 154 LEU ASN ASP MET GLY ASP THR PRO LEU HIS ARG ALA ALA SEQRES 8 B 154 PHE THR GLY ARG LYS GLU LEU VAL MET LEU LEU LEU GLU SEQRES 9 B 154 TYR ASN ALA ASP THR THR ILE VAL ASN GLY SER GLY GLN SEQRES 10 B 154 THR ALA LYS GLU VAL THR HIS ALA GLU GLU ILE ARG SER SEQRES 11 B 154 MET LEU GLU ALA VAL GLU ARG THR GLN GLN ARG LYS LEU SEQRES 12 B 154 GLU GLU LEU LEU LEU ALA ALA ALA ARG GLU GLY SEQRES 1 C 199 GLY SER ALA MET GLY SER THR SER ARG LYS LYS VAL LEU SEQRES 2 C 199 LEU LYS VAL ILE ILE LEU GLY ASP SER GLY VAL GLY LYS SEQRES 3 C 199 THR SER LEU MET ASN GLN TYR VAL ASN LYS LYS PHE SER SEQRES 4 C 199 ASN GLN TYR LYS ALA THR ILE GLY ALA ASP PHE LEU THR SEQRES 5 C 199 LYS GLU VAL MET VAL ASP ASP ARG LEU VAL THR MET GLN SEQRES 6 C 199 ILE TRP ASP THR ALA GLY LEU GLU ARG PHE GLN SER GLY SEQRES 7 C 199 VAL ALA PHE TYR ARG GLY ALA ASP CYS CYS VAL LEU VAL SEQRES 8 C 199 PHE ASP VAL THR ALA PRO ASN THR PHE LYS THR LEU ASP SEQRES 9 C 199 SER TRP ARG ASP GLU PHE LEU ILE GLN ALA SER PRO ARG SEQRES 10 C 199 ASP PRO GLU ASN PHE PRO PHE VAL VAL LEU GLY ASN LYS SEQRES 11 C 199 ILE ASP LEU GLU ASN ARG GLN VAL ALA THR LYS ARG ALA SEQRES 12 C 199 GLN ALA TRP CYS TYR SER LYS ASN ASN ILE PRO TYR PHE SEQRES 13 C 199 GLU THR SER ALA LYS GLU ALA ILE ASN VAL GLU GLN ALA SEQRES 14 C 199 PHE GLN THR ILE ALA ARG ASN ALA LEU LYS GLN GLU THR SEQRES 15 C 199 GLU VAL GLU LEU TYR ASN GLU PHE PRO GLU PRO ILE LYS SEQRES 16 C 199 LEU ASP LYS ASN SEQRES 1 D 154 GLY SER ALA MET GLY SER ALA GLU GLN GLN LEU LEU HIS SEQRES 2 D 154 HIS ALA ARG ASN GLY ASN ALA GLU GLU VAL ARG GLN LEU SEQRES 3 D 154 LEU GLU THR MET ALA ARG ASN GLU VAL ILE ALA ASP ILE SEQRES 4 D 154 ASN CYS LYS GLY ARG SER LYS SER ASN LEU GLY TRP THR SEQRES 5 D 154 PRO LEU HIS LEU ALA CYS TYR PHE GLY HIS ARG GLN VAL SEQRES 6 D 154 VAL GLN ASP LEU LEU LYS ALA GLY ALA GLU VAL ASN VAL SEQRES 7 D 154 LEU ASN ASP MET GLY ASP THR PRO LEU HIS ARG ALA ALA SEQRES 8 D 154 PHE THR GLY ARG LYS GLU LEU VAL MET LEU LEU LEU GLU SEQRES 9 D 154 TYR ASN ALA ASP THR THR ILE VAL ASN GLY SER GLY GLN SEQRES 10 D 154 THR ALA LYS GLU VAL THR HIS ALA GLU GLU ILE ARG SER SEQRES 11 D 154 MET LEU GLU ALA VAL GLU ARG THR GLN GLN ARG LYS LEU SEQRES 12 D 154 GLU GLU LEU LEU LEU ALA ALA ALA ARG GLU GLY HET MG A1301 1 HET GTP A1302 32 HET MG C1301 1 HET GTP C1302 32 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 5 MG 2(MG 2+) FORMUL 6 GTP 2(C10 H16 N5 O14 P3) FORMUL 9 HOH *334(H2 O) HELIX 1 AA1 GLY A 20 LYS A 31 1 12 HELIX 2 AA2 LEU A 67 GLN A 71 5 5 HELIX 3 AA3 VAL A 75 ARG A 79 5 5 HELIX 4 AA4 ALA A 92 THR A 98 1 7 HELIX 5 AA5 THR A 98 SER A 111 1 14 HELIX 6 AA6 ASP A 114 PHE A 118 5 5 HELIX 7 AA7 ALA A 135 LYS A 146 1 12 HELIX 8 AA8 ASN A 161 THR A 178 1 18 HELIX 9 AA9 ALA B 5 GLY B 16 1 12 HELIX 10 AB1 ASN B 17 ALA B 29 1 13 HELIX 11 AB2 THR B 50 GLY B 59 1 10 HELIX 12 AB3 HIS B 60 ALA B 70 1 11 HELIX 13 AB4 THR B 83 THR B 91 1 9 HELIX 14 AB5 ARG B 93 TYR B 103 1 11 HELIX 15 AB6 THR B 116 THR B 121 1 6 HELIX 16 AB7 ALA B 123 GLN B 138 1 16 HELIX 17 AB8 GLY C 20 LYS C 31 1 12 HELIX 18 AB9 LEU C 67 GLN C 71 5 5 HELIX 19 AC1 VAL C 75 ARG C 79 5 5 HELIX 20 AC2 PRO C 93 THR C 98 1 6 HELIX 21 AC3 THR C 98 SER C 111 1 14 HELIX 22 AC4 ASP C 114 PHE C 118 5 5 HELIX 23 AC5 ALA C 135 LYS C 146 1 12 HELIX 24 AC6 ASN C 161 THR C 178 1 18 HELIX 25 AC7 SER D 4 GLY D 16 1 13 HELIX 26 AC8 ASN D 17 ARG D 30 1 14 HELIX 27 AC9 THR D 50 PHE D 58 1 9 HELIX 28 AD1 HIS D 60 ALA D 70 1 11 HELIX 29 AD2 THR D 83 THR D 91 1 9 HELIX 30 AD3 ARG D 93 TYR D 103 1 11 HELIX 31 AD4 THR D 116 THR D 121 1 6 HELIX 32 AD5 ALA D 123 GLN D 137 1 15 SHEET 1 AA1 6 ALA A 43 VAL A 52 0 SHEET 2 AA1 6 ARG A 55 THR A 64 -1 O MET A 59 N LYS A 48 SHEET 3 AA1 6 LEU A 8 LEU A 14 1 N LEU A 9 O GLN A 60 SHEET 4 AA1 6 CYS A 83 ASP A 89 1 O VAL A 85 N ILE A 12 SHEET 5 AA1 6 PHE A 120 ASN A 125 1 O VAL A 121 N LEU A 86 SHEET 6 AA1 6 TYR A 151 GLU A 153 1 O PHE A 152 N GLY A 124 SHEET 1 AA2 6 ALA C 43 MET C 51 0 SHEET 2 AA2 6 LEU C 56 THR C 64 -1 O VAL C 57 N VAL C 50 SHEET 3 AA2 6 LEU C 8 GLY C 15 1 N LEU C 9 O GLN C 60 SHEET 4 AA2 6 CYS C 83 ASP C 89 1 O VAL C 85 N ILE C 12 SHEET 5 AA2 6 PHE C 120 ASN C 125 1 O VAL C 121 N LEU C 86 SHEET 6 AA2 6 TYR C 151 GLU C 153 1 O PHE C 152 N VAL C 122 LINK OG1 THR A 22 MG MG A1301 1555 1555 2.16 LINK OG1 THR A 40 MG MG A1301 1555 1555 2.07 LINK MG MG A1301 O3G GTP A1302 1555 1555 2.07 LINK MG MG A1301 O2B GTP A1302 1555 1555 2.03 LINK MG MG A1301 O HOH A1425 1555 1555 2.07 LINK MG MG A1301 O HOH A1431 1555 1555 2.16 LINK OG1 THR C 22 MG MG C1301 1555 1555 1.99 LINK OG1 THR C 40 MG MG C1301 1555 1555 2.13 LINK MG MG C1301 O3G GTP C1302 1555 1555 2.00 LINK MG MG C1301 O1B GTP C1302 1555 1555 1.94 LINK MG MG C1301 O HOH C1403 1555 1555 2.40 LINK MG MG C1301 O HOH C1407 1555 1555 2.09 SITE 1 AC1 5 THR A 22 THR A 40 GTP A1302 HOH A1425 SITE 2 AC1 5 HOH A1431 SITE 1 AC2 25 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC2 25 LYS A 21 THR A 22 SER A 23 PHE A 33 SITE 3 AC2 25 SER A 34 ASN A 35 TYR A 37 THR A 40 SITE 4 AC2 25 GLY A 66 ASN A 125 LYS A 126 ASP A 128 SITE 5 AC2 25 LEU A 129 SER A 155 ALA A 156 LYS A 157 SITE 6 AC2 25 MG A1301 HOH A1413 HOH A1425 HOH A1431 SITE 7 AC2 25 HOH A1458 SITE 1 AC3 5 THR C 22 THR C 40 GTP C1302 HOH C1403 SITE 2 AC3 5 HOH C1407 SITE 1 AC4 24 SER C 17 GLY C 18 VAL C 19 GLY C 20 SITE 2 AC4 24 LYS C 21 THR C 22 SER C 23 PHE C 33 SITE 3 AC4 24 SER C 34 ASN C 35 TYR C 37 THR C 40 SITE 4 AC4 24 GLY C 66 ASN C 125 LYS C 126 ASP C 128 SITE 5 AC4 24 LEU C 129 SER C 155 ALA C 156 LYS C 157 SITE 6 AC4 24 MG C1301 HOH C1403 HOH C1407 HOH C1423 CRYST1 55.136 117.222 130.476 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 0.018137 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008531 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007664 0.00000