HEADER PROTEIN TRANSPORT 13-JAN-06 2FOL TITLE CRYSTAL STRUCTURE OF HUMAN RAB1A IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: YPT1-RELATED PROTEIN; COMPND 5 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: RAB1A, RAB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P28A-LIC KEYWDS G-PROTEIN, RAB, GTP ANALOGUE, STRUCTURAL GENOMICS, STRUCT URAL KEYWDS 2 GENOMICS CONSORTIUM, SGC, STRUCTURAL GENOMICS CONSORTIUM, PROTEIN KEYWDS 3 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,W.TEMPEL,Y.SHEN,L.SHEN,C.ARROWSMITH,A.EDWARDS,M.SUNDSTROM, AUTHOR 2 J.WEIGELT,A.BOCHKAREV,H.PARK,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 5 30-AUG-23 2FOL 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2FOL 1 REMARK REVDAT 3 13-JUL-11 2FOL 1 VERSN REVDAT 2 24-FEB-09 2FOL 1 VERSN REVDAT 1 31-JAN-06 2FOL 0 JRNL AUTH J.WANG,W.TEMPEL,Y.SHEN,L.SHEN,C.ARROWSMITH,A.EDWARDS, JRNL AUTH 2 M.SUNDSTROM,J.WEIGELT,A.BOCHKAREV,H.PARK, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF HUMAN RAB1A IN COMPLEX WITH GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.VAN DEN BEDEM,I.LOTAN,J.-C.LATOMBE,A.M.DEACON REMARK 1 TITL REAL-SPACE PROTEIN-MODEL COMPLETION: AN INVERSE-KINEMATICS REMARK 1 TITL 2 APPROACH. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 61 2 2005 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15608370 REMARK 1 DOI 10.1107/S0907444904025697 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 5048 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.616 REMARK 3 FREE R VALUE TEST SET COUNT : 233 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) : 2.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 356 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4060 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.3960 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1240 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.60300 REMARK 3 B22 (A**2) : -0.60300 REMARK 3 B33 (A**2) : 0.90500 REMARK 3 B12 (A**2) : -0.30200 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.347 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 32.488 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1289 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 852 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1745 ; 1.397 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2087 ; 0.797 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 153 ; 4.754 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 57 ;38.020 ;25.088 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 235 ;16.052 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ;24.925 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 201 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1386 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 257 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 302 ; 0.223 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 879 ; 0.209 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 615 ; 0.191 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 655 ; 0.097 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 66 ; 0.190 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.137 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.167 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.277 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.227 ; 0.500 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): 994 ; 0.459 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 317 ; 0.069 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1237 ; 0.599 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1019 ; 0.268 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 640 ; 0.990 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 766 ; 0.287 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 508 ; 1.662 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1068 ; 0.753 ; 4.500 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 5 A 173 REMARK 3 RESIDUE RANGE : A 201 A 202 REMARK 3 ORIGIN FOR THE GROUP (A): -20.8949 16.5437 5.9051 REMARK 3 T TENSOR REMARK 3 T11: 0.1055 T22: 0.1480 REMARK 3 T33: 0.0975 T12: -0.0740 REMARK 3 T13: -0.0405 T23: -0.1592 REMARK 3 L TENSOR REMARK 3 L11: 3.6219 L22: 3.4933 REMARK 3 L33: 1.2636 L12: -0.2086 REMARK 3 L13: -0.2542 L23: -1.0124 REMARK 3 S TENSOR REMARK 3 S11: -0.0599 S12: 0.5078 S13: -0.3102 REMARK 3 S21: -0.0694 S22: 0.1536 S23: -0.1911 REMARK 3 S31: -0.0182 S32: 0.0678 S33: -0.0937 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 2FOL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 42 REMARK 42 MOLPROBITY STRUCTURE VALIDATION REMARK 42 PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) REMARK 42 AUTHORS : I.W.DAVIS,J.M.WORD REMARK 42 URL : HTTP://KINEMAGE.BIOCHEM.DUKE.EDU/MOLPROBITY/ REMARK 42 AUTHORS : J.S.RICHARDSON,W.B.ARENDALL,D.C.RICHARDSON REMARK 42 REFERENCE : NEW TOOLS AND DATA FOR IMPROVING REMARK 42 : STRUCTURES, USING ALL-ATOM CONTACTS REMARK 42 : METHODS IN ENZYMOLOGY. 2003;374:385-412. REMARK 42 MOLPROBITY OUTPUT SCORES: REMARK 42 ALL-ATOM CLASHSCORE : 18.17 (0.00 B<40) REMARK 42 BAD ROTAMERS : 6.6% 9/137 (TARGET 0-1%) REMARK 42 RAMACHANDRAN OUTLIERS : 0.0% 0/151 (TARGET 0.2%) REMARK 42 RAMACHANDRAN FAVORED : 95.4% 144/151 (TARGET 98.0%) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036123. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5102 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.60 REMARK 200 R MERGE (I) : 0.08800 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) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 10.50 REMARK 200 R MERGE FOR SHELL (I) : 0.82600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 ENTRIES 1YZN, 1UKV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.2M MAGNESIUM CHLORIDE, REMARK 280 0.1M TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 32.72000 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 16.36000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 16.36000 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 32.72000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE REMARK 300 CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 REMARK 300 CHAIN(S). THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. 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 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 UNK UNX A 401 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 -16 REMARK 465 GLY A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 SER A -6 REMARK 465 SER A -5 REMARK 465 GLY A -4 REMARK 465 LEU A -3 REMARK 465 VAL A -2 REMARK 465 PRO A -1 REMARK 465 ARG A 0 REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 GLU A 4 REMARK 465 THR A 64 REMARK 465 ALA A 65 REMARK 465 GLY A 66 REMARK 465 GLN A 67 REMARK 465 GLU A 68 REMARK 465 ARG A 69 REMARK 465 PHE A 70 REMARK 465 ARG A 71 REMARK 465 THR A 72 REMARK 465 ILE A 73 REMARK 465 THR A 74 REMARK 465 SER A 75 REMARK 465 SER A 76 REMARK 465 TYR A 77 REMARK 465 GLY A 174 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 92 UNK UNX A 401 2.12 REMARK 500 O GLY A 42 UNK UNX A 402 2.12 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 GLN A 160 CG GLN A 160 CD 0.143 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 TYR A 33 138.85 -170.29 REMARK 500 LEU A 52 118.73 -164.13 REMARK 500 TYR A 109 66.94 -109.80 REMARK 500 ALA A 110 140.91 -174.03 REMARK 500 SER A 111 134.25 -34.71 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 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 OG REMARK 620 2 GDP A 201 O1B 139.5 REMARK 620 3 GDP A 201 O3B 84.9 58.6 REMARK 620 4 HOH A 301 O 88.7 90.9 113.9 REMARK 620 5 HOH A 302 O 74.1 114.7 84.0 154.3 REMARK 620 6 HOH A 306 O 149.2 58.7 94.3 119.1 75.3 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 MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 402 DBREF 2FOL A 3 174 UNP P62820 RAB1A_HUMAN 5 176 SEQADV 2FOL MET A -16 UNP P62820 CLONING ARTIFACT SEQADV 2FOL GLY A -15 UNP P62820 CLONING ARTIFACT SEQADV 2FOL SER A -14 UNP P62820 CLONING ARTIFACT SEQADV 2FOL SER A -13 UNP P62820 CLONING ARTIFACT SEQADV 2FOL HIS A -12 UNP P62820 EXPRESSION TAG SEQADV 2FOL HIS A -11 UNP P62820 EXPRESSION TAG SEQADV 2FOL HIS A -10 UNP P62820 EXPRESSION TAG SEQADV 2FOL HIS A -9 UNP P62820 EXPRESSION TAG SEQADV 2FOL HIS A -8 UNP P62820 EXPRESSION TAG SEQADV 2FOL HIS A -7 UNP P62820 EXPRESSION TAG SEQADV 2FOL SER A -6 UNP P62820 CLONING ARTIFACT SEQADV 2FOL SER A -5 UNP P62820 CLONING ARTIFACT SEQADV 2FOL GLY A -4 UNP P62820 CLONING ARTIFACT SEQADV 2FOL LEU A -3 UNP P62820 CLONING ARTIFACT SEQADV 2FOL VAL A -2 UNP P62820 CLONING ARTIFACT SEQADV 2FOL PRO A -1 UNP P62820 CLONING ARTIFACT SEQADV 2FOL ARG A 0 UNP P62820 CLONING ARTIFACT SEQADV 2FOL GLY A 1 UNP P62820 CLONING ARTIFACT SEQADV 2FOL SER A 2 UNP P62820 CLONING ARTIFACT SEQRES 1 A 191 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 191 LEU VAL PRO ARG GLY SER PRO GLU TYR ASP TYR LEU PHE SEQRES 3 A 191 LYS LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS SER SEQRES 4 A 191 CYS LEU LEU LEU ARG PHE ALA ASP ASP THR TYR THR GLU SEQRES 5 A 191 SER TYR ILE SER THR ILE GLY VAL ASP PHE LYS ILE ARG SEQRES 6 A 191 THR ILE GLU LEU ASP GLY LYS THR ILE LYS LEU GLN ILE SEQRES 7 A 191 TRP ASP THR ALA GLY GLN GLU ARG PHE ARG THR ILE THR SEQRES 8 A 191 SER SER TYR TYR ARG GLY ALA HIS GLY ILE ILE VAL VAL SEQRES 9 A 191 TYR ASP VAL THR ASP GLN GLU SER PHE ASN ASN VAL LYS SEQRES 10 A 191 GLN TRP LEU GLN GLU ILE ASP ARG TYR ALA SER GLU ASN SEQRES 11 A 191 VAL ASN LYS LEU LEU VAL GLY ASN LYS CYS ASP LEU THR SEQRES 12 A 191 THR LYS LYS VAL VAL ASP TYR THR THR ALA LYS GLU PHE SEQRES 13 A 191 ALA ASP SER LEU GLY ILE PRO PHE LEU GLU THR SER ALA SEQRES 14 A 191 LYS ASN ALA THR ASN VAL GLU GLN SER PHE MET THR MET SEQRES 15 A 191 ALA ALA GLU ILE LYS LYS ARG MET GLY HET MG A 202 1 HET GDP A 201 28 HET UNX A 401 1 HET UNX A 402 1 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 MG MG 2+ FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 UNX 2(X) FORMUL 6 HOH *5(H2 O) HELIX 1 1 GLY A 20 ASP A 31 1 12 HELIX 2 2 ASP A 92 ASN A 98 1 7 HELIX 3 3 ASN A 98 TYR A 109 1 12 HELIX 4 4 ASP A 132 GLY A 144 1 13 HELIX 5 5 ASN A 157 MET A 173 1 17 SHEET 1 A 6 LYS A 46 LEU A 52 0 SHEET 2 A 6 LYS A 55 TRP A 62 -1 O ILE A 61 N LYS A 46 SHEET 3 A 6 TYR A 7 GLY A 15 1 N PHE A 9 O LYS A 58 SHEET 4 A 6 GLY A 83 ASP A 89 1 O ILE A 85 N LEU A 12 SHEET 5 A 6 ASN A 115 ASN A 121 1 O ASN A 115 N ILE A 84 SHEET 6 A 6 PHE A 147 GLU A 149 1 O LEU A 148 N LEU A 118 LINK OG SER A 22 MG MG A 202 1555 1555 2.18 LINK O1B GDP A 201 MG MG A 202 1555 1555 2.70 LINK O3B GDP A 201 MG MG A 202 1555 1555 2.23 LINK MG MG A 202 O HOH A 301 1555 1555 1.85 LINK MG MG A 202 O HOH A 302 1555 1555 2.08 LINK MG MG A 202 O HOH A 306 1555 1555 2.32 SITE 1 AC1 5 SER A 22 GDP A 201 HOH A 301 HOH A 302 SITE 2 AC1 5 HOH A 306 SITE 1 AC2 21 ASP A 16 SER A 17 GLY A 18 VAL A 19 SITE 2 AC2 21 GLY A 20 LYS A 21 SER A 22 CYS A 23 SITE 3 AC2 21 TYR A 33 GLU A 35 ASN A 121 LYS A 122 SITE 4 AC2 21 ASP A 124 LEU A 125 SER A 151 ALA A 152 SITE 5 AC2 21 LYS A 153 MG A 202 HOH A 301 HOH A 302 SITE 6 AC2 21 HOH A 306 SITE 1 AC3 1 ASP A 92 SITE 1 AC4 6 GLY A 42 VAL A 43 ALA A 81 HIS A 82 SITE 2 AC4 6 SER A 111 ARG A 172 CRYST1 75.790 75.790 49.080 90.00 90.00 120.00 P 32 2 1 6 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 0.013190 0.007620 0.000000 0.00000 SCALE2 0.000000 0.015240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020380 0.00000