PDB Short entry for 2OT3 HEADER PROTEIN TRANSPORT 07-FEB-07 2OT3 TITLE CRYSTAL STRUCTURE OF RABEX-5 VPS9 DOMAIN IN COMPLEX WITH NUCLEOTIDE TITLE 2 FREE RAB21 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB5 GDP/GTP EXCHANGE FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 132-297; COMPND 5 SYNONYM: RABEX-5, RABAPTIN-5-ASSOCIATED EXCHANGE FACTOR FOR RAB5, COMPND 6 RAP1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RAS-RELATED PROTEIN RAB-21; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: RESIDUES 16-183; 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: RABGEF1, RABEX5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RAB21, KIAA0118; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX4T1 KEYWDS RABEX-5, VPS9 DOMAIN, RAB21, VESICULAR TRAFFIC, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.DELPRATO,D.LAMBRIGHT REVDAT 5 30-AUG-23 2OT3 1 REMARK SEQADV REVDAT 4 11-OCT-17 2OT3 1 REMARK REVDAT 3 24-FEB-09 2OT3 1 VERSN REVDAT 2 22-MAY-07 2OT3 1 JRNL REVDAT 1 24-APR-07 2OT3 0 JRNL AUTH A.DELPRATO,D.G.LAMBRIGHT JRNL TITL STRUCTURAL BASIS FOR RAB GTPASE ACTIVATION BY VPS9 DOMAIN JRNL TITL 2 EXCHANGE FACTORS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 406 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17450153 JRNL DOI 10.1038/NSMB1232 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28020 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 + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1500 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2022 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3179 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 463 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.17000 REMARK 3 B22 (A**2) : -0.33000 REMARK 3 B33 (A**2) : 1.50000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.209 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.187 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.125 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.642 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3234 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4372 ; 1.230 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 5.240 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 136 ;37.856 ;24.412 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 572 ;14.620 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.829 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 502 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2392 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1761 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2274 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 432 ; 0.195 ; 0.200 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): 49 ; 0.179 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 48 ; 0.179 ; 0.200 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): 2105 ; 0.858 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3277 ; 1.486 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1285 ; 1.994 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1095 ; 3.211 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2OT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041551. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI(11) REMARK 200 OPTICS : PT-COATED TOROIDAL SI MIRROR FOR REMARK 200 HORIZONTAL AND VERTICAL REMARK 200 FOCUSSING FOLLOWED BY DOUBLE REMARK 200 FLAT SI CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40412 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 7.50000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 38.5000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 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: PDB ENTRY 1Z0I, 1TXU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 6000, 0.2M MGCL2, 0.05 NAMES REMARK 280 MICROSEEDED, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 35.94850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.70000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.94850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.70000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 124 REMARK 465 SER A 125 REMARK 465 HIS A 126 REMARK 465 HIS A 127 REMARK 465 HIS A 128 REMARK 465 HIS A 129 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 SER A 132 REMARK 465 ILE A 133 REMARK 465 GLU A 134 REMARK 465 THR A 135 REMARK 465 ASP A 136 REMARK 465 ARG A 137 REMARK 465 VAL A 138 REMARK 465 ARG A 392 REMARK 465 LYS A 393 REMARK 465 GLN A 394 REMARK 465 GLU A 395 REMARK 465 ALA A 396 REMARK 465 GLU A 397 REMARK 465 GLY B 14 REMARK 465 SER B 15 REMARK 465 ARG B 16 REMARK 465 GLU B 41 REMARK 465 ASN B 42 REMARK 465 LYS B 43 REMARK 465 PHE B 44 REMARK 465 ASN B 45 REMARK 465 ASP B 46 REMARK 465 LYS B 47 REMARK 465 HIS B 48 REMARK 465 ILE B 49 REMARK 465 THR B 183 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 LYS A 140 CG CD CE NZ REMARK 470 HIS A 150 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 151 CG CD CE NZ REMARK 470 THR A 152 OG1 CG2 REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 GLN A 159 CG CD OE1 NE2 REMARK 470 HIS A 168 CG ND1 CD2 CE1 NE2 REMARK 470 TYR A 169 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG A 171 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 GLU A 177 CG CD OE1 OE2 REMARK 470 HIS A 187 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 191 CG CD OE1 OE2 REMARK 470 ARG A 192 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 196 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 202 CG CD OE1 OE2 REMARK 470 GLU A 205 CG CD OE1 OE2 REMARK 470 LYS A 206 CG CD CE NZ REMARK 470 LYS A 221 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 GLU A 277 CG CD OE1 OE2 REMARK 470 THR B 50 OG1 CG2 REMARK 470 LYS B 60 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 ARG B 67 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 137 CG CD OE1 OE2 REMARK 470 LYS B 138 CG CD CE NZ REMARK 470 GLU B 152 CG CD OE1 OE2 REMARK 470 GLN B 165 CG CD OE1 NE2 REMARK 470 ASN B 166 CG OD1 ND2 REMARK 470 GLU B 170 CG CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 HIS A 187 CB 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 HIS A 187 CB - CA - C ANGL. DEV. = 15.7 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 HIS A 150 -128.85 56.69 REMARK 500 THR A 152 -34.35 -156.05 REMARK 500 THR A 195 -94.10 -69.79 REMARK 500 LYS A 198 73.02 42.15 REMARK 500 ASN A 327 59.61 37.08 REMARK 500 THR A 349 -35.51 -132.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1TXU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE VPS9 DOMAIN OF RABEX-5 REMARK 900 RELATED ID: 1Z0I RELATED DB: PDB REMARK 900 GDP-BOUND RAB21 GTPASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN SEQUENCE MATCHES TO ISOFORM 2 OF THE UNP REMARK 999 REFERENCE DBREF 2OT3 A 132 397 UNP Q9UJ41 RABX5_HUMAN 132 397 DBREF 2OT3 B 16 183 UNP Q9UL25 RAB21_HUMAN 16 183 SEQADV 2OT3 GLY A 124 UNP Q9UJ41 CLONING ARTIFACT SEQADV 2OT3 SER A 125 UNP Q9UJ41 CLONING ARTIFACT SEQADV 2OT3 HIS A 126 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 HIS A 127 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 HIS A 128 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 HIS A 129 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 HIS A 130 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 HIS A 131 UNP Q9UJ41 EXPRESSION TAG SEQADV 2OT3 GLY B 14 UNP Q9UL25 CLONING ARTIFACT SEQADV 2OT3 SER B 15 UNP Q9UL25 CLONING ARTIFACT SEQRES 1 A 274 GLY SER HIS HIS HIS HIS HIS HIS SER ILE GLU THR ASP SEQRES 2 A 274 ARG VAL SER LYS GLU PHE ILE GLU PHE LEU LYS THR PHE SEQRES 3 A 274 HIS LYS THR GLY GLN GLU ILE TYR LYS GLN THR LYS LEU SEQRES 4 A 274 PHE LEU GLU GLY MET HIS TYR LYS ARG ASP LEU SER ILE SEQRES 5 A 274 GLU GLU GLN SER GLU CYS ALA GLN ASP PHE TYR HIS ASN SEQRES 6 A 274 VAL ALA GLU ARG MET GLN THR ARG GLY LYS VAL PRO PRO SEQRES 7 A 274 GLU ARG VAL GLU LYS ILE MET ASP GLN ILE GLU LYS TYR SEQRES 8 A 274 ILE MET THR ARG LEU TYR LYS TYR VAL PHE CYS PRO GLU SEQRES 9 A 274 THR THR ASP ASP GLU LYS LYS ASP LEU ALA ILE GLN LYS SEQRES 10 A 274 ARG ILE ARG ALA LEU ARG TRP VAL THR PRO GLN MET LEU SEQRES 11 A 274 CYS VAL PRO VAL ASN GLU ASP ILE PRO GLU VAL SER ASP SEQRES 12 A 274 MET VAL VAL LYS ALA ILE THR ASP ILE ILE GLU MET ASP SEQRES 13 A 274 SER LYS ARG VAL PRO ARG ASP LYS LEU ALA CYS ILE THR SEQRES 14 A 274 LYS CYS SER LYS HIS ILE PHE ASN ALA ILE LYS ILE THR SEQRES 15 A 274 LYS ASN GLU PRO ALA SER ALA ASP ASP PHE LEU PRO THR SEQRES 16 A 274 LEU ILE TYR ILE VAL LEU LYS GLY ASN PRO PRO ARG LEU SEQRES 17 A 274 GLN SER ASN ILE GLN TYR ILE THR ARG PHE CYS ASN PRO SEQRES 18 A 274 SER ARG LEU MET THR GLY GLU ASP GLY TYR TYR PHE THR SEQRES 19 A 274 ASN LEU CYS CYS ALA VAL ALA PHE ILE GLU LYS LEU ASP SEQRES 20 A 274 ALA GLN SER LEU ASN LEU SER GLN GLU ASP PHE ASP ARG SEQRES 21 A 274 TYR MET SER GLY GLN THR SER PRO ARG LYS GLN GLU ALA SEQRES 22 A 274 GLU SEQRES 1 B 170 GLY SER ARG ALA TYR SER PHE LYS VAL VAL LEU LEU GLY SEQRES 2 B 170 GLU GLY CYS VAL GLY LYS THR SER LEU VAL LEU ARG TYR SEQRES 3 B 170 CYS GLU ASN LYS PHE ASN ASP LYS HIS ILE THR THR LEU SEQRES 4 B 170 GLN ALA SER PHE LEU THR LYS LYS LEU ASN ILE GLY GLY SEQRES 5 B 170 LYS ARG VAL ASN LEU ALA ILE TRP ASP THR ALA GLY GLN SEQRES 6 B 170 GLU ARG PHE HIS ALA LEU GLY PRO ILE TYR TYR ARG ASP SEQRES 7 B 170 SER ASN GLY ALA ILE LEU VAL TYR ASP ILE THR ASP GLU SEQRES 8 B 170 ASP SER PHE GLN LYS VAL LYS ASN TRP VAL LYS GLU LEU SEQRES 9 B 170 ARG LYS MET LEU GLY ASN GLU ILE CYS LEU CYS ILE VAL SEQRES 10 B 170 GLY ASN LYS ILE ASP LEU GLU LYS GLU ARG HIS VAL SER SEQRES 11 B 170 ILE GLN GLU ALA GLU SER TYR ALA GLU SER VAL GLY ALA SEQRES 12 B 170 LYS HIS TYR HIS THR SER ALA LYS GLN ASN LYS GLY ILE SEQRES 13 B 170 GLU GLU LEU PHE LEU ASP LEU CYS LYS ARG MET ILE GLU SEQRES 14 B 170 THR FORMUL 3 HOH *463(H2 O) HELIX 1 1 GLU A 141 THR A 148 1 8 HELIX 2 2 PHE A 149 PHE A 149 5 1 HELIX 3 3 GLY A 153 GLN A 154 5 2 HELIX 4 4 ILE A 156 LYS A 158 5 3 HELIX 5 5 THR A 160 MET A 167 1 8 HELIX 6 6 GLN A 178 TYR A 186 1 9 HELIX 7 7 ASN A 188 ALA A 190 5 3 HELIX 8 8 ILE A 207 TYR A 220 1 14 HELIX 9 9 TYR A 222 PHE A 224 5 3 HELIX 10 10 ASP A 230 GLN A 239 1 10 HELIX 11 11 ARG A 241 ARG A 246 5 6 HELIX 12 12 ILE A 261 ILE A 276 1 16 HELIX 13 13 VAL A 283 ASN A 307 1 25 HELIX 14 14 SER A 311 ASN A 327 1 17 HELIX 15 15 ARG A 330 CYS A 342 1 13 HELIX 16 16 GLY A 350 LEU A 369 1 20 HELIX 17 17 ALA A 371 ASN A 375 5 5 HELIX 18 18 SER A 377 SER A 386 1 10 HELIX 19 19 GLU B 27 VAL B 30 5 4 HELIX 20 20 GLY B 31 CYS B 40 1 10 HELIX 21 21 GLN B 78 ALA B 83 5 6 HELIX 22 22 LEU B 84 ARG B 90 1 7 HELIX 23 23 ASP B 103 ARG B 118 1 16 HELIX 24 24 SER B 143 ALA B 151 1 9 HELIX 25 25 GLU B 171 GLU B 182 1 12 SHEET 1 A 6 PHE B 56 LYS B 59 0 SHEET 2 A 6 ASN B 69 ASP B 74 -1 O ILE B 72 N LEU B 57 SHEET 3 A 6 SER B 19 LEU B 25 1 N VAL B 22 O TRP B 73 SHEET 4 A 6 GLY B 94 ASP B 100 1 O ILE B 96 N LEU B 25 SHEET 5 A 6 CYS B 126 ASN B 132 1 O CYS B 128 N LEU B 97 SHEET 6 A 6 LYS B 157 HIS B 160 1 O LYS B 157 N ILE B 129 CRYST1 71.897 113.400 60.533 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 0.013909 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008818 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016520 0.00000