HEADER PROTEIN TRANSPORT 10-JAN-05 1YHN TITLE STRUCTURE BASIS OF RILP RECRUITMENT BY RAB7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-7; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RAB7; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAB INTERACTING LYSOSOMAL PROTEIN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RILP EFFECTOR DOMAIN; COMPND 11 SYNONYM: RILP; 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: RAB7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21*; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RILP; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL-21*; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS RILP, RAB7, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.WU,T.WANG,W.HONG,H.SONG REVDAT 3 13-JUL-11 1YHN 1 VERSN REVDAT 2 24-FEB-09 1YHN 1 VERSN REVDAT 1 17-MAY-05 1YHN 0 JRNL AUTH M.WU,T.WANG,E.LOH,W.HONG,H.SONG JRNL TITL STRUCTURAL BASIS FOR RECRUITMENT OF RILP BY SMALL GTPASE JRNL TITL 2 RAB7. JRNL REF EMBO J. V. 24 1491 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15933719 JRNL DOI 10.1038/SJ.EMBOJ.7600643 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 6904 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2014 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.00 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.009 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; 0.000 ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.682 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; 3.529 ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1YHN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031521. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : BW7A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9175 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL FOCUSING REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7272 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 51.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.300 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.09700 REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.40 REMARK 200 R MERGE FOR SHELL (I) : 0.42600 REMARK 200 R SYM FOR SHELL (I) : 0.42600 REMARK 200 FOR SHELL : 1.800 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: PDB ENTRY 1T91 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, POLYVINYLPYRROLIDONE REMARK 280 K15, HEPS, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.55067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 44.27533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.41300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.13767 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 110.68833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 88.55067 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 44.27533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 22.13767 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 66.41300 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 110.68833 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE REMARK 300 MONOMER IN THE ASYMMETRIC UNIT BY SYMMETRIC OPERATION. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 10810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.41300 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 THR A 2 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 ASP A 196 REMARK 465 ARG A 197 REMARK 465 ALA A 198 REMARK 465 LYS A 199 REMARK 465 ALA A 200 REMARK 465 SER A 201 REMARK 465 ALA A 202 REMARK 465 GLU A 203 REMARK 465 SER A 204 REMARK 465 CYS A 205 REMARK 465 SER A 206 REMARK 465 CYS A 207 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 OD2 ASP A 54 O HOH A 317 2.04 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 320 O HOH A 320 8675 1.82 REMARK 500 N SER B 244 N SER B 244 11555 2.02 REMARK 500 CD1 LEU B 276 CD1 LEU B 276 11555 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 LYS A 38 63.14 -174.96 REMARK 500 ALA A 39 118.54 -12.96 REMARK 500 ALA A 43 131.06 176.62 REMARK 500 ASP A 53 74.86 64.19 REMARK 500 ASP A 54 7.81 53.86 REMARK 500 ARG A 69 37.75 -80.45 REMARK 500 PHE A 70 -9.50 -163.52 REMARK 500 GLN A 71 33.41 -71.80 REMARK 500 SER A 72 -103.91 -40.14 REMARK 500 LEU A 73 -82.38 -25.06 REMARK 500 VAL A 75 74.17 -48.37 REMARK 500 ALA A 76 42.88 21.05 REMARK 500 ALA A 81 104.58 4.67 REMARK 500 GLN A 109 -72.66 -75.43 REMARK 500 ASP A 114 60.58 65.14 REMARK 500 ILE A 127 -7.29 -55.78 REMARK 500 ARG A 132 112.28 -167.83 REMARK 500 LYS A 146 -117.11 -78.59 REMARK 500 ASN A 147 58.13 -116.62 REMARK 500 ASN A 161 13.89 59.85 REMARK 500 GLU A 177 -1.21 59.22 REMARK 500 LEU A 182 -131.99 -116.94 REMARK 500 ARG B 245 114.54 -34.64 REMARK 500 GLU B 249 6.14 -65.76 REMARK 500 GLN B 250 -69.66 -99.94 REMARK 500 THR B 278 -150.02 -77.70 REMARK 500 ARG B 281 155.28 -4.92 REMARK 500 VAL B 282 143.43 168.51 REMARK 500 PRO B 283 150.20 -24.65 REMARK 500 SER B 284 -101.69 -85.38 REMARK 500 LEU B 285 -32.32 -26.73 REMARK 500 LYS B 300 -77.36 -48.83 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 A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 301 O1G REMARK 620 2 GTP A 301 O3B 49.9 REMARK 620 3 THR A 64 O 103.7 103.3 REMARK 620 4 THR A 22 OG1 86.6 100.1 155.9 REMARK 620 5 THR A 40 OG1 56.5 105.5 103.2 64.1 REMARK 620 6 ASP A 63 OD1 173.0 134.5 70.7 97.1 119.9 REMARK 620 7 ASP A 63 OD2 136.2 154.2 98.7 60.5 82.1 43.4 REMARK 620 N 1 2 3 4 5 6 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 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T91 RELATED DB: PDB REMARK 900 RAB7-GTP DBREF 1YHN B 244 308 UNP Q96NA2 RILP_HUMAN 244 308 DBREF 1YHN A 1 207 UNP P51149 RAB7_HUMAN 1 207 SEQADV 1YHN LEU A 67 UNP P51149 GLN 67 ENGINEERED 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 LEU 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 ASP ARG ALA LYS ALA SER ALA GLU SER CYS SER CYS SEQRES 1 B 65 SER ARG GLU GLU PHE GLU GLN ILE LEU GLN GLU ARG ASN SEQRES 2 B 65 GLU LEU LYS ALA LYS VAL PHE LEU LEU LYS GLU GLU LEU SEQRES 3 B 65 ALA TYR PHE GLN ARG GLU LEU LEU THR ASP HIS ARG VAL SEQRES 4 B 65 PRO SER LEU LEU LEU GLU ALA MET LYS VAL ALA VAL ARG SEQRES 5 B 65 LYS GLN ARG LYS LYS ILE LYS ALA LYS MET LEU GLY THR HET MG A 302 1 HET GTP A 301 32 HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 GTP C10 H16 N5 O14 P3 FORMUL 5 HOH *34(H2 O) HELIX 1 1 GLY A 20 LYS A 31 1 12 HELIX 2 2 LEU A 67 GLN A 71 5 5 HELIX 3 3 PRO A 93 THR A 98 1 6 HELIX 4 4 THR A 98 SER A 111 1 14 HELIX 5 5 ASP A 114 PHE A 118 5 5 HELIX 6 6 ALA A 135 LYS A 146 1 12 HELIX 7 7 ASN A 161 LYS A 175 1 15 HELIX 8 8 GLU B 247 LEU B 277 1 31 HELIX 9 9 PRO B 283 GLY B 307 1 25 SHEET 1 A 6 ALA A 43 MET A 51 0 SHEET 2 A 6 LEU A 56 THR A 64 -1 O MET A 59 N LYS A 48 SHEET 3 A 6 LYS A 6 LEU A 14 1 N LEU A 9 O GLN A 60 SHEET 4 A 6 CYS A 83 ASP A 89 1 O VAL A 85 N LEU A 14 SHEET 5 A 6 PHE A 120 ASN A 125 1 O LEU A 123 N PHE A 88 SHEET 6 A 6 TYR A 151 GLU A 153 1 O PHE A 152 N GLY A 124 SHEET 1 B 4 ALA A 43 MET A 51 0 SHEET 2 B 4 LEU A 56 THR A 64 -1 O MET A 59 N LYS A 48 SHEET 3 B 4 LYS A 6 LEU A 14 1 N LEU A 9 O GLN A 60 SHEET 4 B 4 VAL A 180 GLU A 181 -1 O VAL A 180 N LEU A 8 LINK MG MG A 302 O1G GTP A 301 1555 1555 2.80 LINK MG MG A 302 O3B GTP A 301 1555 1555 3.09 LINK MG MG A 302 O THR A 64 1555 1555 3.07 LINK MG MG A 302 OG1 THR A 22 1555 1555 2.23 LINK MG MG A 302 OG1 THR A 40 1555 1555 2.51 LINK MG MG A 302 OD1 ASP A 63 1555 1555 2.81 LINK MG MG A 302 OD2 ASP A 63 1555 1555 3.11 SITE 1 AC1 5 THR A 22 THR A 40 ASP A 63 THR A 64 SITE 2 AC1 5 GTP A 301 SITE 1 AC2 24 SER A 17 GLY A 18 VAL A 19 GLY A 20 SITE 2 AC2 24 LYS A 21 THR A 22 SER A 23 PHE A 33 SITE 3 AC2 24 SER A 34 ASN A 35 TYR A 37 THR A 40 SITE 4 AC2 24 THR A 64 ALA A 65 GLY A 66 ASN A 125 SITE 5 AC2 24 LYS A 126 ASP A 128 LEU A 129 SER A 155 SITE 6 AC2 24 ALA A 156 LYS A 157 MG A 302 HOH A 311 CRYST1 93.134 93.134 132.826 90.00 90.00 120.00 P 65 2 2 12 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 0.010737 0.006199 0.000000 0.00000 SCALE2 0.000000 0.012398 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007529 0.00000 MASTER 409 0 2 9 10 0 8 6 0 0 0 21 END