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 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,VAGIN,DODSON 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 HOH A 301 O REMARK 620 2 HOH A 302 O 154.3 REMARK 620 3 HOH A 306 O 119.1 75.3 REMARK 620 4 SER A 22 OG 88.7 74.1 149.2 REMARK 620 5 GDP A 201 O1B 90.9 114.7 58.7 139.5 REMARK 620 6 GDP A 201 O3B 113.9 84.0 94.3 84.9 58.6 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 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 LINK MG MG A 202 OG SER A 22 1555 1555 2.18 LINK MG MG A 202 O1B GDP A 201 1555 1555 2.70 LINK MG MG A 202 O3B GDP A 201 1555 1555 2.23 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 MASTER 418 0 4 5 6 0 11 6 0 0 0 15 END