PDB Short entry for 1YHN 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 5 25-OCT-23 1YHN 1 REMARK REVDAT 4 10-NOV-21 1YHN 1 REMARK SEQADV LINK 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,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER 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 DEPOSITION ID IS D_1000031521. 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 : SCALA, 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 : 11.30 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : 0.09700 REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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 REMARK 280 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 THR A 22 OG1 REMARK 620 2 THR A 40 OG1 64.1 REMARK 620 3 ASP A 63 OD1 97.1 119.9 REMARK 620 4 ASP A 63 OD2 60.5 82.1 43.4 REMARK 620 5 THR A 64 O 155.9 103.2 70.7 98.7 REMARK 620 6 GTP A 301 O1G 86.6 56.5 173.0 136.2 103.7 REMARK 620 7 GTP A 301 O3B 100.1 105.5 134.5 154.2 103.3 49.9 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 MUTATION 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 OG1 THR A 22 MG MG A 302 1555 1555 2.23 LINK OG1 THR A 40 MG MG A 302 1555 1555 2.51 LINK OD1 ASP A 63 MG MG A 302 1555 1555 2.81 LINK OD2 ASP A 63 MG MG A 302 1555 1555 3.11 LINK O THR A 64 MG MG A 302 1555 1555 3.07 LINK O1G GTP A 301 MG MG A 302 1555 1555 2.80 LINK O3B GTP A 301 MG MG A 302 1555 1555 3.09 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