HEADER PROTEIN TRANSPORT 04-FEB-12 4DKX TITLE CRYSTAL STRUCTURE OF THE RAB 6A'(Q72L) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-6A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RAB GTPASE, RAB-6; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAB6A, RAB6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS GTP BINDING FOLD, MEMBRANE TRAFFICKING, GTP, CYTOSOL, PROTEIN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.H.PARK,Y.-C.SHIN REVDAT 2 20-MAR-24 4DKX 1 REMARK SEQADV LINK REVDAT 1 17-OCT-12 4DKX 0 JRNL AUTH Y.-C.SHIN,J.H.YOON,T.-H.JANG,S.Y.KIM,W.D.HEO,I.SO,J.-H.JEON, JRNL AUTH 2 H.H.PARK JRNL TITL CRYSTAL STRUCTURE OF RAB6A'(Q72L) MUTANT REVEALS UNEXPECTED JRNL TITL 2 GDP/MG2+ BINDING WITH OPENED GTP-BINDING DOMAIN JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 424 269 2012 JRNL REFN ISSN 0006-291X JRNL PMID 22750005 JRNL DOI 10.1016/J.BBRC.2012.06.102 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 30283 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1613 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2198 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3130 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 247 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 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): 0.145 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.093 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2587 ; 0.028 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3495 ; 3.175 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 303 ; 6.436 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;33.166 ;23.109 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 479 ;15.633 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;22.384 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 398 ; 0.188 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1867 ; 0.010 ; 0.020 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): 1520 ; 1.399 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2458 ; 2.381 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1067 ; 4.061 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1037 ; 6.234 ; 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 : 1.40 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 4DKX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070458. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31899 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 48.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 70.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 200MM CALCIUM ACETATE, REMARK 280 100MM SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.99850 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.39000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 54.99850 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: MONOMERIC 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 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 HOH A 439 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 MET A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 GLY A 4 REMARK 465 GLY A 5 REMARK 465 ASP A 6 REMARK 465 PHE A 7 REMARK 465 GLY A 8 REMARK 465 ASN A 9 REMARK 465 PRO A 10 REMARK 465 LEU A 11 REMARK 465 ARG A 12 REMARK 465 ASN A 40 REMARK 465 THR A 41 REMARK 465 TYR A 42 REMARK 465 GLN A 43 REMARK 465 ALA A 44 REMARK 465 THR A 45 REMARK 465 ILE A 46 REMARK 465 GLY A 47 REMARK 465 ILE A 48 REMARK 465 ASP A 49 REMARK 465 PRO A 175 REMARK 465 GLY A 176 REMARK 465 MET A 177 REMARK 465 GLU A 178 REMARK 465 SER A 179 REMARK 465 THR A 180 REMARK 465 GLN A 181 REMARK 465 ASP A 182 REMARK 465 ARG A 183 REMARK 465 SER A 184 REMARK 465 ARG A 185 REMARK 465 GLU A 186 REMARK 465 ASP A 187 REMARK 465 MET A 188 REMARK 465 ILE A 189 REMARK 465 ASP A 190 REMARK 465 ILE A 191 REMARK 465 LYS A 192 REMARK 465 LEU A 193 REMARK 465 GLU A 194 REMARK 465 LYS A 195 REMARK 465 PRO A 196 REMARK 465 GLN A 197 REMARK 465 GLU A 198 REMARK 465 GLN A 199 REMARK 465 PRO A 200 REMARK 465 VAL A 201 REMARK 465 SER A 202 REMARK 465 GLU A 203 REMARK 465 GLY A 204 REMARK 465 GLY A 205 REMARK 465 CYS A 206 REMARK 465 SER A 207 REMARK 465 CYS A 208 REMARK 465 LEU A 209 REMARK 465 GLU A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214 REMARK 465 HIS A 215 REMARK 465 HIS A 216 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 GLY B 4 REMARK 465 GLY B 5 REMARK 465 ASP B 6 REMARK 465 PHE B 7 REMARK 465 GLY B 8 REMARK 465 ASN B 9 REMARK 465 PRO B 10 REMARK 465 LEU B 11 REMARK 465 ASP B 39 REMARK 465 ASN B 40 REMARK 465 THR B 41 REMARK 465 TYR B 42 REMARK 465 GLN B 43 REMARK 465 ALA B 44 REMARK 465 THR B 45 REMARK 465 ILE B 46 REMARK 465 GLY B 47 REMARK 465 GLY B 176 REMARK 465 MET B 177 REMARK 465 GLU B 178 REMARK 465 SER B 179 REMARK 465 THR B 180 REMARK 465 GLN B 181 REMARK 465 ASP B 182 REMARK 465 ARG B 183 REMARK 465 SER B 184 REMARK 465 ARG B 185 REMARK 465 GLU B 186 REMARK 465 ASP B 187 REMARK 465 MET B 188 REMARK 465 ILE B 189 REMARK 465 ASP B 190 REMARK 465 ILE B 191 REMARK 465 LYS B 192 REMARK 465 LEU B 193 REMARK 465 GLU B 194 REMARK 465 LYS B 195 REMARK 465 PRO B 196 REMARK 465 GLN B 197 REMARK 465 GLU B 198 REMARK 465 GLN B 199 REMARK 465 PRO B 200 REMARK 465 VAL B 201 REMARK 465 SER B 202 REMARK 465 GLU B 203 REMARK 465 GLY B 204 REMARK 465 GLY B 205 REMARK 465 CYS B 206 REMARK 465 SER B 207 REMARK 465 CYS B 208 REMARK 465 LEU B 209 REMARK 465 GLU B 210 REMARK 465 HIS B 211 REMARK 465 HIS B 212 REMARK 465 HIS B 213 REMARK 465 HIS B 214 REMARK 465 HIS B 215 REMARK 465 HIS B 216 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 C LEU A 174 O HOH A 494 1.90 REMARK 500 OD1 ASP B 85 O HOH B 468 1.96 REMARK 500 N PHE A 50 O HOH A 437 2.01 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 OD1 ASP B 49 O HOH A 515 4654 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 112 CZ ARG A 112 NH2 0.092 REMARK 500 GLU A 140 CG GLU A 140 CD 0.114 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 85 C - N - CA ANGL. DEV. = -17.2 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 VAL B 17 CG1 - CB - CG2 ANGL. DEV. = 12.6 DEGREES REMARK 500 ARG B 84 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 ASP B 85 C - N - CA ANGL. DEV. = -26.8 DEGREES REMARK 500 ASP B 94 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 143 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG B 143 NE - CZ - NH2 ANGL. DEV. = 8.0 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 SER A 23 10.71 83.29 REMARK 500 PHE A 75 64.52 -112.95 REMARK 500 ASP A 118 49.73 -84.32 REMARK 500 LYS A 127 34.68 77.59 REMARK 500 ASP B 36 53.27 39.79 REMARK 500 LYS B 127 36.00 79.95 REMARK 500 LEU B 130 45.77 -97.44 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 27 OG1 REMARK 620 2 GDP A 301 O2B 84.1 REMARK 620 3 HOH A 518 O 83.9 83.7 REMARK 620 4 HOH A 519 O 170.6 86.5 94.8 REMARK 620 5 HOH A 520 O 85.5 93.1 169.2 95.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 27 OG1 REMARK 620 2 GDP B 302 O3B 80.6 REMARK 620 3 HOH B 525 O 84.3 82.9 REMARK 620 4 HOH B 526 O 172.7 92.7 97.5 REMARK 620 5 HOH B 527 O 83.1 89.4 166.2 94.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 302 REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 62-88 ARE BASED ON ISOFORM 2 OF RAB6A_HUMAN (P20340). REMARK 999 RESIDUES 62, 87 AND 88 ARE ILE, ALA AND ALA RESPECTIVELY IN ISOFORM REMARK 999 2. DBREF 4DKX A 1 208 UNP P20340 RAB6A_HUMAN 1 208 DBREF 4DKX B 1 208 UNP P20340 RAB6A_HUMAN 1 208 SEQADV 4DKX ILE A 62 UNP P20340 VAL 62 SEE REMARK 999 SEQADV 4DKX LEU A 72 UNP P20340 GLN 72 ENGINEERED MUTATION SEQADV 4DKX ALA A 87 UNP P20340 THR 87 SEE REMARK 999 SEQADV 4DKX ALA A 88 UNP P20340 VAL 88 SEE REMARK 999 SEQADV 4DKX LEU A 209 UNP P20340 EXPRESSION TAG SEQADV 4DKX GLU A 210 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 211 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 212 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 213 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 214 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 215 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS A 216 UNP P20340 EXPRESSION TAG SEQADV 4DKX ILE B 62 UNP P20340 VAL 62 SEE REMARK 999 SEQADV 4DKX LEU B 72 UNP P20340 GLN 72 ENGINEERED MUTATION SEQADV 4DKX ALA B 87 UNP P20340 THR 87 SEE REMARK 999 SEQADV 4DKX ALA B 88 UNP P20340 VAL 88 SEE REMARK 999 SEQADV 4DKX LEU B 209 UNP P20340 EXPRESSION TAG SEQADV 4DKX GLU B 210 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 211 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 212 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 213 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 214 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 215 UNP P20340 EXPRESSION TAG SEQADV 4DKX HIS B 216 UNP P20340 EXPRESSION TAG SEQRES 1 A 216 MET SER THR GLY GLY ASP PHE GLY ASN PRO LEU ARG LYS SEQRES 2 A 216 PHE LYS LEU VAL PHE LEU GLY GLU GLN SER VAL GLY LYS SEQRES 3 A 216 THR SER LEU ILE THR ARG PHE MET TYR ASP SER PHE ASP SEQRES 4 A 216 ASN THR TYR GLN ALA THR ILE GLY ILE ASP PHE LEU SER SEQRES 5 A 216 LYS THR MET TYR LEU GLU ASP ARG THR ILE ARG LEU GLN SEQRES 6 A 216 LEU TRP ASP THR ALA GLY LEU GLU ARG PHE ARG SER LEU SEQRES 7 A 216 ILE PRO SER TYR ILE ARG ASP SER ALA ALA ALA VAL VAL SEQRES 8 A 216 VAL TYR ASP ILE THR ASN VAL ASN SER PHE GLN GLN THR SEQRES 9 A 216 THR LYS TRP ILE ASP ASP VAL ARG THR GLU ARG GLY SER SEQRES 10 A 216 ASP VAL ILE ILE MET LEU VAL GLY ASN LYS THR ASP LEU SEQRES 11 A 216 ALA ASP LYS ARG GLN VAL SER ILE GLU GLU GLY GLU ARG SEQRES 12 A 216 LYS ALA LYS GLU LEU ASN VAL MET PHE ILE GLU THR SER SEQRES 13 A 216 ALA LYS ALA GLY TYR ASN VAL LYS GLN LEU PHE ARG ARG SEQRES 14 A 216 VAL ALA ALA ALA LEU PRO GLY MET GLU SER THR GLN ASP SEQRES 15 A 216 ARG SER ARG GLU ASP MET ILE ASP ILE LYS LEU GLU LYS SEQRES 16 A 216 PRO GLN GLU GLN PRO VAL SER GLU GLY GLY CYS SER CYS SEQRES 17 A 216 LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 216 MET SER THR GLY GLY ASP PHE GLY ASN PRO LEU ARG LYS SEQRES 2 B 216 PHE LYS LEU VAL PHE LEU GLY GLU GLN SER VAL GLY LYS SEQRES 3 B 216 THR SER LEU ILE THR ARG PHE MET TYR ASP SER PHE ASP SEQRES 4 B 216 ASN THR TYR GLN ALA THR ILE GLY ILE ASP PHE LEU SER SEQRES 5 B 216 LYS THR MET TYR LEU GLU ASP ARG THR ILE ARG LEU GLN SEQRES 6 B 216 LEU TRP ASP THR ALA GLY LEU GLU ARG PHE ARG SER LEU SEQRES 7 B 216 ILE PRO SER TYR ILE ARG ASP SER ALA ALA ALA VAL VAL SEQRES 8 B 216 VAL TYR ASP ILE THR ASN VAL ASN SER PHE GLN GLN THR SEQRES 9 B 216 THR LYS TRP ILE ASP ASP VAL ARG THR GLU ARG GLY SER SEQRES 10 B 216 ASP VAL ILE ILE MET LEU VAL GLY ASN LYS THR ASP LEU SEQRES 11 B 216 ALA ASP LYS ARG GLN VAL SER ILE GLU GLU GLY GLU ARG SEQRES 12 B 216 LYS ALA LYS GLU LEU ASN VAL MET PHE ILE GLU THR SER SEQRES 13 B 216 ALA LYS ALA GLY TYR ASN VAL LYS GLN LEU PHE ARG ARG SEQRES 14 B 216 VAL ALA ALA ALA LEU PRO GLY MET GLU SER THR GLN ASP SEQRES 15 B 216 ARG SER ARG GLU ASP MET ILE ASP ILE LYS LEU GLU LYS SEQRES 16 B 216 PRO GLN GLU GLN PRO VAL SER GLU GLY GLY CYS SER CYS SEQRES 17 B 216 LEU GLU HIS HIS HIS HIS HIS HIS HET GDP A 301 28 HET MG A 302 1 HET MG B 301 1 HET GDP B 302 28 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MG 2(MG 2+) FORMUL 7 HOH *247(H2 O) HELIX 1 1 GLY A 25 ASP A 36 1 12 HELIX 2 2 PHE A 75 SER A 77 5 3 HELIX 3 3 LEU A 78 ARG A 84 1 7 HELIX 4 4 ASN A 97 GLN A 103 1 7 HELIX 5 5 GLN A 103 GLY A 116 1 14 HELIX 6 6 LEU A 130 ARG A 134 5 5 HELIX 7 7 SER A 137 ASN A 149 1 13 HELIX 8 8 ASN A 162 LEU A 174 1 13 HELIX 9 9 GLY B 25 ASP B 36 1 12 HELIX 10 10 GLY B 71 SER B 77 5 7 HELIX 11 11 LEU B 78 ARG B 84 1 7 HELIX 12 12 ASN B 97 GLY B 116 1 20 HELIX 13 13 THR B 128 ARG B 134 5 7 HELIX 14 14 SER B 137 ASN B 149 1 13 HELIX 15 15 ASN B 162 ALA B 173 1 12 SHEET 1 A 6 LEU A 51 TYR A 56 0 SHEET 2 A 6 THR A 61 TRP A 67 -1 O ILE A 62 N MET A 55 SHEET 3 A 6 PHE A 14 LEU A 19 1 N PHE A 14 O GLN A 65 SHEET 4 A 6 ALA A 88 ASP A 94 1 O VAL A 92 N LEU A 19 SHEET 5 A 6 ILE A 120 ASN A 126 1 O ASN A 126 N TYR A 93 SHEET 6 A 6 MET A 151 THR A 155 1 O MET A 151 N LEU A 123 SHEET 1 B 6 ASP B 49 LEU B 57 0 SHEET 2 B 6 ARG B 60 ASP B 68 -1 O ILE B 62 N MET B 55 SHEET 3 B 6 LYS B 13 GLY B 20 1 N PHE B 14 O GLN B 65 SHEET 4 B 6 ALA B 88 ASP B 94 1 O VAL B 92 N LEU B 19 SHEET 5 B 6 ILE B 120 ASN B 126 1 O ASN B 126 N TYR B 93 SHEET 6 B 6 MET B 151 THR B 155 1 O MET B 151 N LEU B 123 LINK OG1 THR A 27 MG MG A 302 1555 1555 2.45 LINK O2B GDP A 301 MG MG A 302 1555 1555 2.33 LINK MG MG A 302 O HOH A 518 1555 1555 2.16 LINK MG MG A 302 O HOH A 519 1555 1555 2.31 LINK MG MG A 302 O HOH A 520 1555 1555 2.50 LINK OG1 THR B 27 MG MG B 301 1555 1555 2.25 LINK MG MG B 301 O3B GDP B 302 1555 1555 2.26 LINK MG MG B 301 O HOH B 525 1555 1555 2.11 LINK MG MG B 301 O HOH B 526 1555 1555 2.27 LINK MG MG B 301 O HOH B 527 1555 1555 2.33 SITE 1 AC1 19 SER A 23 VAL A 24 GLY A 25 LYS A 26 SITE 2 AC1 19 THR A 27 SER A 28 PHE A 38 ASP A 39 SITE 3 AC1 19 ASN A 126 LYS A 127 ASP A 129 LEU A 130 SITE 4 AC1 19 SER A 156 ALA A 157 LYS A 158 MG A 302 SITE 5 AC1 19 HOH A 454 HOH A 518 HOH A 519 SITE 1 AC2 5 THR A 27 GDP A 301 HOH A 518 HOH A 519 SITE 2 AC2 5 HOH A 520 SITE 1 AC3 5 THR B 27 GDP B 302 HOH B 525 HOH B 526 SITE 2 AC3 5 HOH B 527 SITE 1 AC4 19 SER B 23 VAL B 24 GLY B 25 LYS B 26 SITE 2 AC4 19 THR B 27 SER B 28 PHE B 38 ASN B 126 SITE 3 AC4 19 LYS B 127 ASP B 129 LEU B 130 SER B 156 SITE 4 AC4 19 ALA B 157 LYS B 158 MG B 301 HOH B 410 SITE 5 AC4 19 HOH B 480 HOH B 525 HOH B 526 CRYST1 36.838 96.780 109.997 90.00 90.00 90.00 P 2 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 0.027146 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010333 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009091 0.00000