HEADER PROTEIN TRANSPORT 02-FEB-04 1S8F TITLE CRYSTAL STRUCTURE OF RAB9 COMPLEXED TO GDP REVEALS A DIMER WITH AN TITLE 2 ACTIVE CONFORMATION OF SWITCH II COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-9A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RAB-9, RAB9 GTPASE; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: C-TERMINAL TRUNCATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANIS LUPUS FAMILIARIS; SOURCE 3 ORGANISM_COMMON: DOG; SOURCE 4 ORGANISM_TAXID: 9615; SOURCE 5 STRAIN: FAMILIARIS; SOURCE 6 GENE: RAB9A, RAB9; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTRACELLULAR TRANSPORT, VESICULAR TRAFFICKING, HEMIHEDRAL TWINNING, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.G.WITTMANN,M.G.RUDOLPH REVDAT 4 23-AUG-23 1S8F 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1S8F 1 VERSN REVDAT 2 22-JUN-04 1S8F 1 JRNL AUTHOR REVDAT 1 11-JUN-04 1S8F 0 JRNL AUTH J.G.WITTMANN,M.G.RUDOLPH JRNL TITL CRYSTAL STRUCTURE OF RAB9 COMPLEXED TO GDP REVEALS A DIMER JRNL TITL 2 WITH AN ACTIVE CONFORMATION OF SWITCH II. JRNL REF FEBS LETT. V. 568 23 2004 JRNL REFN ISSN 0014-5793 JRNL PMID 15196914 JRNL DOI 10.1016/J.FEBSLET.2004.05.004 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : KEEP TWIN-RELATED REFLECTION REMARK 3 IN SAME SET REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.165 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1825 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35770 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31429 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 231 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3027.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2550.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 4 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 12164 REMARK 3 NUMBER OF RESTRAINTS : 11650 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.033 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.039 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.080 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURE WAS REFINED AGAINST DATA FROM A HEMIHEDRALLY TWINNED REMARK 3 CRYSTAL. THE TWIN FRACTION IS 0.253, THE TWIN OPERATOR IS (K,H,-L). REMARK 4 REMARK 4 1S8F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1000021497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 1.0091 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37662 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.06910 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COMO REMARK 200 STARTING MODEL: PDB ENTRY 1KY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8000, NA-BENZOATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 49.12250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 49.12250 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.83000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.12250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.91500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.12250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 59.74500 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 49.12250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.12250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 39.83000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 49.12250 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 59.74500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 49.12250 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.91500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -222.0 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 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -81.0 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 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 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 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 SR SR B2001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A9012 LIES ON A SPECIAL POSITION. 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 999 REMARK 465 ALA A 1000 REMARK 465 MET A 1001 REMARK 465 ALA A 1002 REMARK 465 GLY A 1003 REMARK 465 LYS A 1004 REMARK 465 LYS A 1112 REMARK 465 GLU A 1113 REMARK 465 THR A 1175 REMARK 465 THR B 4034 REMARK 465 GLN B 4035 REMARK 465 ALA B 4174 REMARK 465 THR B 4175 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 VAL A1111 CG1 CG2 REMARK 470 LYS B4031 CG CD CE NZ REMARK 470 LYS B4112 CG CD CE NZ REMARK 470 GLU B4113 CG CD OE1 OE2 REMARK 470 GLU B4115 CG CD OE1 OE2 REMARK 470 GLU B4130 CG CD OE1 OE2 REMARK 470 ARG B4170 CG CD NE CZ NH1 NH2 REMARK 470 ARG B4171 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A1073 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 LEU B4012 CA - CB - CG ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP B4015 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B4073 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG B4073 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B4131 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A1110 71.90 47.32 REMARK 500 ALA A1158 -4.60 80.17 REMARK 500 ASN A1160 13.56 57.79 REMARK 500 PRO B4118 91.26 -65.01 REMARK 500 LYS B4125 35.57 74.90 REMARK 500 ASP B4127 11.92 -68.09 REMARK 500 GLU B4130 58.19 170.72 REMARK 500 ALA B4158 -5.77 82.47 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 SR A2401 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A1021 OG REMARK 620 2 BEZ A1502 O1 147.9 REMARK 620 3 BEZ A1502 O2 135.3 51.3 REMARK 620 4 GDP A3400 O2B 127.6 84.2 72.4 REMARK 620 5 GDP A3400 O3B 78.1 132.7 111.3 49.7 REMARK 620 6 GDP A3400 O1A 101.0 86.2 123.4 67.0 68.2 REMARK 620 7 HOH A9005 O 74.3 80.2 74.8 146.6 143.7 140.0 REMARK 620 8 HOH A9009 O 72.2 119.3 68.9 88.1 74.9 143.1 74.5 REMARK 620 9 HOH A9024 O 84.1 70.1 116.8 127.4 126.3 66.2 73.8 144.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 SR B2001 SR REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B4071 N REMARK 620 2 SER B4071 OG 53.6 REMARK 620 3 SER B4071 OG 134.7 87.8 REMARK 620 4 SER B4071 N 171.2 134.7 53.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B5401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B4021 OG REMARK 620 2 GDP B6400 O3B 85.8 REMARK 620 3 HOH B9007 O 92.8 79.7 REMARK 620 4 HOH B9015 O 93.0 176.2 96.8 REMARK 620 5 HOH B9019 O 175.4 89.9 88.0 91.3 REMARK 620 6 HOH B9033 O 97.1 91.3 166.1 92.4 81.4 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 SR A 2401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 5401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SR B 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 3400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 6400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEZ B 1503 DBREF 1S8F A 1000 1174 UNP P24408 RAB9A_CANFA 1 175 DBREF 1S8F B 4000 4174 UNP P24408 RAB9A_CANFA 1 175 SEQADV 1S8F GLY A 999 UNP P24408 CLONING ARTIFACT SEQADV 1S8F ALA A 1000 UNP P24408 CLONING ARTIFACT SEQADV 1S8F GLY B 3999 UNP P24408 CLONING ARTIFACT SEQADV 1S8F ALA B 4000 UNP P24408 CLONING ARTIFACT SEQRES 1 A 177 GLY ALA MET ALA GLY LYS SER SER LEU PHE LYS VAL ILE SEQRES 2 A 177 LEU LEU GLY ASP GLY GLY VAL GLY LYS SER SER LEU MET SEQRES 3 A 177 ASN ARG TYR VAL THR ASN LYS PHE ASP THR GLN LEU PHE SEQRES 4 A 177 HIS THR ILE GLY VAL GLU PHE LEU ASN LYS ASP LEU GLU SEQRES 5 A 177 VAL ASP GLY HIS PHE VAL THR MET GLN ILE TRP ASP THR SEQRES 6 A 177 ALA GLY GLN GLU ARG PHE ARG SER LEU ARG THR PRO PHE SEQRES 7 A 177 TYR ARG GLY SER ASP CYS CYS LEU LEU THR PHE SER VAL SEQRES 8 A 177 ASP ASP SER GLN SER PHE GLN ASN LEU SER ASN TRP LYS SEQRES 9 A 177 LYS GLU PHE ILE TYR TYR ALA ASP VAL LYS GLU PRO GLU SEQRES 10 A 177 SER PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE ASP ILE SEQRES 11 A 177 SER GLU ARG GLN VAL SER THR GLU GLU ALA GLN ALA TRP SEQRES 12 A 177 CYS ARG ASP ASN GLY ASP TYR PRO TYR PHE GLU THR SER SEQRES 13 A 177 ALA LYS ASP ALA THR ASN VAL ALA ALA ALA PHE GLU GLU SEQRES 14 A 177 ALA VAL ARG ARG VAL LEU ALA THR SEQRES 1 B 177 GLY ALA MET ALA GLY LYS SER SER LEU PHE LYS VAL ILE SEQRES 2 B 177 LEU LEU GLY ASP GLY GLY VAL GLY LYS SER SER LEU MET SEQRES 3 B 177 ASN ARG TYR VAL THR ASN LYS PHE ASP THR GLN LEU PHE SEQRES 4 B 177 HIS THR ILE GLY VAL GLU PHE LEU ASN LYS ASP LEU GLU SEQRES 5 B 177 VAL ASP GLY HIS PHE VAL THR MET GLN ILE TRP ASP THR SEQRES 6 B 177 ALA GLY GLN GLU ARG PHE ARG SER LEU ARG THR PRO PHE SEQRES 7 B 177 TYR ARG GLY SER ASP CYS CYS LEU LEU THR PHE SER VAL SEQRES 8 B 177 ASP ASP SER GLN SER PHE GLN ASN LEU SER ASN TRP LYS SEQRES 9 B 177 LYS GLU PHE ILE TYR TYR ALA ASP VAL LYS GLU PRO GLU SEQRES 10 B 177 SER PHE PRO PHE VAL ILE LEU GLY ASN LYS ILE ASP ILE SEQRES 11 B 177 SER GLU ARG GLN VAL SER THR GLU GLU ALA GLN ALA TRP SEQRES 12 B 177 CYS ARG ASP ASN GLY ASP TYR PRO TYR PHE GLU THR SER SEQRES 13 B 177 ALA LYS ASP ALA THR ASN VAL ALA ALA ALA PHE GLU GLU SEQRES 14 B 177 ALA VAL ARG ARG VAL LEU ALA THR HET SR A2401 1 HET GDP A3400 28 HET BEZ A1500 9 HET BEZ A1501 9 HET BEZ A1502 9 HET MG B5401 1 HET SR B2001 1 HET CL B3001 1 HET GDP B6400 28 HET BEZ B1503 9 HETNAM SR STRONTIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM BEZ BENZOIC ACID HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 3 SR 2(SR 2+) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 5 BEZ 4(C7 H6 O2) FORMUL 8 MG MG 2+ FORMUL 10 CL CL 1- FORMUL 13 HOH *231(H2 O) HELIX 1 1 GLY A 1019 ASN A 1030 1 12 HELIX 2 2 GLN A 1066 ARG A 1068 5 3 HELIX 3 3 PHE A 1069 THR A 1074 1 6 HELIX 4 4 PRO A 1075 TYR A 1077 5 3 HELIX 5 5 ASP A 1091 ASN A 1097 1 7 HELIX 6 6 ASN A 1097 ASP A 1110 1 14 HELIX 7 7 SER A 1134 ASN A 1145 1 12 HELIX 8 8 ASN A 1160 ALA A 1174 1 15 HELIX 9 9 GLY B 4019 ASN B 4030 1 12 HELIX 10 10 PHE B 4069 ARG B 4078 1 10 HELIX 11 11 ASP B 4091 ASN B 4097 1 7 HELIX 12 12 ASN B 4097 ALA B 4109 1 13 HELIX 13 13 GLU B 4113 PHE B 4117 5 5 HELIX 14 14 SER B 4134 ASN B 4145 1 12 HELIX 15 15 ASN B 4160 LEU B 4173 1 14 SHEET 1 A12 TYR A1150 GLU A1152 0 SHEET 2 A12 PHE A1119 ASN A1124 1 N ILE A1121 O PHE A1151 SHEET 3 A12 CYS A1082 SER A1088 1 N PHE A1087 O ASN A1124 SHEET 4 A12 LEU A1007 LEU A1013 1 N LEU A1013 O THR A1086 SHEET 5 A12 HIS A1054 THR A1063 1 O TRP A1061 N VAL A1010 SHEET 6 A12 HIS A1038 VAL A1051 -1 N LEU A1049 O VAL A1056 SHEET 7 A12 HIS B4038 VAL B4051 -1 O ILE B4040 N VAL A1042 SHEET 8 A12 HIS B4054 ALA B4064 -1 O MET B4058 N LYS B4047 SHEET 9 A12 SER B4005 LEU B4013 1 N SER B4006 O PHE B4055 SHEET 10 A12 CYS B4082 SER B4088 1 O THR B4086 N LEU B4013 SHEET 11 A12 PHE B4119 ASN B4124 1 O ASN B4124 N PHE B4087 SHEET 12 A12 TYR B4150 GLU B4152 1 O PHE B4151 N ILE B4121 LINK OG SER A1021 SR SR A2401 1555 1555 2.70 LINK O1 BEZ A1502 SR SR A2401 1555 1555 2.67 LINK O2 BEZ A1502 SR SR A2401 1555 1555 2.61 LINK SR SR A2401 O2B GDP A3400 1555 1555 3.09 LINK SR SR A2401 O3B GDP A3400 1555 1555 2.38 LINK SR SR A2401 O1A GDP A3400 1555 1555 2.78 LINK SR SR A2401 O HOH A9005 1555 1555 2.69 LINK SR SR A2401 O HOH A9009 1555 1555 2.61 LINK SR SR A2401 O HOH A9024 1555 1555 2.34 LINK SR SR B2001 N SER B4071 1555 1555 3.32 LINK SR SR B2001 OG SER B4071 1555 1555 3.04 LINK SR SR B2001 OG SER B4071 1555 6555 3.04 LINK SR SR B2001 N SER B4071 1555 6555 3.32 LINK OG SER B4021 MG MG B5401 1555 1555 1.89 LINK MG MG B5401 O3B GDP B6400 1555 1555 2.20 LINK MG MG B5401 O HOH B9007 1555 1555 1.84 LINK MG MG B5401 O HOH B9015 1555 1555 2.03 LINK MG MG B5401 O HOH B9019 1555 1555 1.98 LINK MG MG B5401 O HOH B9033 1555 1555 1.78 SITE 1 AC1 6 SER A1021 BEZ A1502 GDP A3400 HOH A9005 SITE 2 AC1 6 HOH A9009 HOH A9024 SITE 1 AC2 6 SER B4021 GDP B6400 HOH B9007 HOH B9015 SITE 2 AC2 6 HOH B9019 HOH B9033 SITE 1 AC3 3 PHE B4069 ARG B4070 SER B4071 SITE 1 AC4 5 ARG B4070 ARG B4073 THR B4074 HOH B9011 SITE 2 AC4 5 HOH B9069 SITE 1 AC5 23 GLY A1017 VAL A1018 GLY A1019 LYS A1020 SITE 2 AC5 23 SER A1021 SER A1022 PHE A1032 ASN A1124 SITE 3 AC5 23 LYS A1125 ASP A1127 ILE A1128 SER A1154 SITE 4 AC5 23 ALA A1155 LYS A1156 BEZ A1502 SR A2401 SITE 5 AC5 23 HOH A9009 HOH A9024 HOH A9026 HOH A9081 SITE 6 AC5 23 HOH A9085 HOH A9152 HOH A9224 SITE 1 AC6 21 GLY B4017 VAL B4018 GLY B4019 LYS B4020 SITE 2 AC6 21 SER B4021 SER B4022 PHE B4032 ASN B4124 SITE 3 AC6 21 LYS B4125 ASP B4127 SER B4154 ALA B4155 SITE 4 AC6 21 LYS B4156 MG B5401 HOH B9007 HOH B9019 SITE 5 AC6 21 HOH B9033 HOH B9095 HOH B9145 HOH B9150 SITE 6 AC6 21 HOH B9219 SITE 1 AC7 9 ARG A1068 PHE A1069 ARG A1070 SER A1071 SITE 2 AC7 9 LEU A1072 BEZ A1501 HOH A9103 SER B4071 SITE 3 AC7 9 HOH B9043 SITE 1 AC8 8 PHE A1055 ARG A1068 BEZ A1500 HOH A9023 SITE 2 AC8 8 HOH A9048 HOH A9116 PRO B4075 HOH B9017 SITE 1 AC9 9 HIS A1038 THR A1039 GLN A1066 SR A2401 SITE 2 AC9 9 GDP A3400 HOH A9009 HOH A9010 HOH A9024 SITE 3 AC9 9 HOH A9054 SITE 1 BC1 7 THR B4063 GLU B4067 ARG B4068 PHE B4069 SITE 2 BC1 7 ARG B4070 ARG B4073 HOH B9110 CRYST1 98.245 98.245 79.660 90.00 90.00 90.00 I 41 16 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 0.010179 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010179 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012553 0.00000