HEADER PROTEIN TRANSPORT 05-DEC-06 2O52 TITLE CRYSTAL STRUCTURE OF HUMAN RAB4B IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-4B; COMPND 3 CHAIN: A, B; COMPND 4 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: RAB4B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE-3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P28A-THROMBIN-LIC KEYWDS G-PROTEIN, RAB, GDP, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHU,W.TEMPEL,J.WANG,Y.SHEN,R.LANDRY,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 M.SUNDSTROM,J.WEIGELT,A.BOCHKAREV,H.PARK,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 4 30-AUG-23 2O52 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2O52 1 REMARK REVDAT 2 24-FEB-09 2O52 1 VERSN REVDAT 1 19-DEC-06 2O52 0 JRNL AUTH H.ZHU,W.TEMPEL,J.WANG,Y.SHEN,R.LANDRY,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,M.SUNDSTROM,J.WEIGELT,A.BOCHKAREV,H.PARK JRNL TITL CRYSTAL STRUCTURE OF HUMAN RAB4B IN COMPLEX WITH GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 21799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.739 REMARK 3 FREE R VALUE TEST SET COUNT : 1033 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 0 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2507 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 75 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) : 1.46600 REMARK 3 B22 (A**2) : 1.46600 REMARK 3 B33 (A**2) : -2.93200 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): 0.247 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.148 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.688 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2651 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1762 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3593 ; 1.409 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4280 ; 0.907 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 331 ; 6.431 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;39.851 ;23.860 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;15.358 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;19.032 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 415 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2917 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 564 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 503 ; 0.198 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1738 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1277 ; 0.172 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1364 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 104 ; 0.147 ; 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): 16 ; 0.117 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.299 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 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): 1677 ; 2.456 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 671 ; 0.653 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2597 ; 3.663 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1143 ; 2.394 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 991 ; 3.256 ; 3.000 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 BULK SOLVENT 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 2O52 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000040696. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40474 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 : 6.200 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.97600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 ENTRY 2BME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG8000, 0.2M MAGNESIUM ACETATE, REMARK 280 0.1M SODIUM CACODYLATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 89.97750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.76400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.76400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 134.96625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.76400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.76400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 44.98875 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.76400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.76400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 134.96625 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.76400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.76400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.98875 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 89.97750 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 AUTHOR STATES THAT BIOLOGICAL UNIT REMARK 300 FOR THE PROTEIN IS NOT YET KNOWN 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 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 ILE A 3 REMARK 465 TRP A 4 REMARK 465 ASN A 31 REMARK 465 LYS A 32 REMARK 465 PHE A 33 REMARK 465 LYS A 34 REMARK 465 GLN A 35 REMARK 465 ASP A 36 REMARK 465 SER A 37 REMARK 465 ASN A 38 REMARK 465 HIS A 39 REMARK 465 THR A 40 REMARK 465 ILE A 41 REMARK 465 GLY A 42 REMARK 465 MET B -16 REMARK 465 GLY B -15 REMARK 465 SER B -14 REMARK 465 SER B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 SER B -6 REMARK 465 SER B -5 REMARK 465 GLY B -4 REMARK 465 LEU B -3 REMARK 465 VAL B -2 REMARK 465 PRO B -1 REMARK 465 ARG B 0 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 ILE B 3 REMARK 465 TRP B 4 REMARK 465 ASN B 31 REMARK 465 LYS B 32 REMARK 465 PHE B 33 REMARK 465 LYS B 34 REMARK 465 GLN B 35 REMARK 465 ASP B 36 REMARK 465 SER B 37 REMARK 465 ASN B 38 REMARK 465 HIS B 39 REMARK 465 THR B 40 REMARK 465 ILE B 41 REMARK 465 GLY B 42 REMARK 465 SER B 175 REMARK 465 GLY B 176 REMARK 465 GLU B 177 REMARK 465 LEU B 178 REMARK 465 ASP B 179 REMARK 465 PRO B 180 REMARK 465 GLU B 181 REMARK 465 ARG B 182 REMARK 465 MET 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 GLU A 30 CG CD OE1 OE2 REMARK 470 ARG A 69 CD NE CZ NH1 NH2 REMARK 470 ARG A 138 NE CZ NH1 NH2 REMARK 470 LYS A 164 CE NZ REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 ARG A 182 CD NE CZ NH1 NH2 REMARK 470 GLU B 30 CG CD OE1 OE2 REMARK 470 ARG B 75 NE CZ NH1 NH2 REMARK 470 LEU B 134 CG CD1 CD2 REMARK 470 ARG B 138 CZ NH1 NH2 REMARK 470 GLU B 142 CG CD OE1 OE2 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 SG CYS B 23 S2 BME B 603 2.07 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 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 89 CB - CG - OD1 ANGL. DEV. = 6.0 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 ALA A 110 -81.84 -90.32 REMARK 500 LYS A 122 33.34 75.87 REMARK 500 LEU A 125 44.83 -96.60 REMARK 500 ALA B 110 -74.89 -96.74 REMARK 500 SER B 111 145.30 -179.31 REMARK 500 ILE B 173 43.41 -83.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BME A 603 REMARK 610 BME B 603 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 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 22 OG REMARK 620 2 GDP A 601 O2B 88.1 REMARK 620 3 HOH A1004 O 88.2 176.3 REMARK 620 4 HOH A1005 O 89.4 82.6 96.7 REMARK 620 5 HOH A1006 O 173.3 89.1 94.4 84.2 REMARK 620 6 HOH A1007 O 85.2 92.1 88.3 172.6 101.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 22 OG REMARK 620 2 GDP B 601 O2B 93.5 REMARK 620 3 HOH B 604 O 88.3 86.5 REMARK 620 4 HOH B 605 O 83.2 170.7 84.7 REMARK 620 5 HOH B 606 O 173.3 91.1 87.1 91.5 REMARK 620 6 HOH B 607 O 86.4 99.3 172.4 89.2 97.7 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 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1003 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE ARE FROM ISOFORM 2: P61018-2 DBREF 2O52 A 6 183 UNP P61018 RAB4B_HUMAN 6 183 DBREF 2O52 B 6 183 UNP P61018 RAB4B_HUMAN 6 183 SEQADV 2O52 MET A -16 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY A -15 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER A -14 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER A -13 UNP P61018 CLONING ARTIFACT SEQADV 2O52 HIS A -12 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS A -11 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS A -10 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS A -9 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS A -8 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS A -7 UNP P61018 EXPRESSION TAG SEQADV 2O52 SER A -6 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER A -5 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY A -4 UNP P61018 CLONING ARTIFACT SEQADV 2O52 LEU A -3 UNP P61018 CLONING ARTIFACT SEQADV 2O52 VAL A -2 UNP P61018 CLONING ARTIFACT SEQADV 2O52 PRO A -1 UNP P61018 CLONING ARTIFACT SEQADV 2O52 ARG A 0 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY A 1 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER A 2 UNP P61018 CLONING ARTIFACT SEQADV 2O52 ILE A 3 UNP P61018 SEE REMARK 999 SEQADV 2O52 TRP A 4 UNP P61018 SEE REMARK 999 SEQADV 2O52 SER A 5 UNP P61018 SEE REMARK 999 SEQADV 2O52 MET B -16 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY B -15 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER B -14 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER B -13 UNP P61018 CLONING ARTIFACT SEQADV 2O52 HIS B -12 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS B -11 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS B -10 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS B -9 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS B -8 UNP P61018 EXPRESSION TAG SEQADV 2O52 HIS B -7 UNP P61018 EXPRESSION TAG SEQADV 2O52 SER B -6 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER B -5 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY B -4 UNP P61018 CLONING ARTIFACT SEQADV 2O52 LEU B -3 UNP P61018 CLONING ARTIFACT SEQADV 2O52 VAL B -2 UNP P61018 CLONING ARTIFACT SEQADV 2O52 PRO B -1 UNP P61018 CLONING ARTIFACT SEQADV 2O52 ARG B 0 UNP P61018 CLONING ARTIFACT SEQADV 2O52 GLY B 1 UNP P61018 CLONING ARTIFACT SEQADV 2O52 SER B 2 UNP P61018 CLONING ARTIFACT SEQADV 2O52 ILE B 3 UNP P61018 SEE REMARK 999 SEQADV 2O52 TRP B 4 UNP P61018 SEE REMARK 999 SEQADV 2O52 SER B 5 UNP P61018 SEE REMARK 999 SEQRES 1 A 200 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 200 LEU VAL PRO ARG GLY SER ILE TRP SER ASP PHE LEU PHE SEQRES 3 A 200 LYS PHE LEU VAL ILE GLY SER ALA GLY THR GLY LYS SER SEQRES 4 A 200 CYS LEU LEU HIS GLN PHE ILE GLU ASN LYS PHE LYS GLN SEQRES 5 A 200 ASP SER ASN HIS THR ILE GLY VAL GLU PHE GLY SER ARG SEQRES 6 A 200 VAL VAL ASN VAL GLY GLY LYS THR VAL LYS LEU GLN ILE SEQRES 7 A 200 TRP ASP THR ALA GLY GLN GLU ARG PHE ARG SER VAL THR SEQRES 8 A 200 ARG SER TYR TYR ARG GLY ALA ALA GLY ALA LEU LEU VAL SEQRES 9 A 200 TYR ASP ILE THR SER ARG GLU THR TYR ASN SER LEU ALA SEQRES 10 A 200 ALA TRP LEU THR ASP ALA ARG THR LEU ALA SER PRO ASN SEQRES 11 A 200 ILE VAL VAL ILE LEU CYS GLY ASN LYS LYS ASP LEU ASP SEQRES 12 A 200 PRO GLU ARG GLU VAL THR PHE LEU GLU ALA SER ARG PHE SEQRES 13 A 200 ALA GLN GLU ASN GLU LEU MET PHE LEU GLU THR SER ALA SEQRES 14 A 200 LEU THR GLY GLU ASN VAL GLU GLU ALA PHE LEU LYS CYS SEQRES 15 A 200 ALA ARG THR ILE LEU ASN LYS ILE ASP SER GLY GLU LEU SEQRES 16 A 200 ASP PRO GLU ARG MET SEQRES 1 B 200 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 200 LEU VAL PRO ARG GLY SER ILE TRP SER ASP PHE LEU PHE SEQRES 3 B 200 LYS PHE LEU VAL ILE GLY SER ALA GLY THR GLY LYS SER SEQRES 4 B 200 CYS LEU LEU HIS GLN PHE ILE GLU ASN LYS PHE LYS GLN SEQRES 5 B 200 ASP SER ASN HIS THR ILE GLY VAL GLU PHE GLY SER ARG SEQRES 6 B 200 VAL VAL ASN VAL GLY GLY LYS THR VAL LYS LEU GLN ILE SEQRES 7 B 200 TRP ASP THR ALA GLY GLN GLU ARG PHE ARG SER VAL THR SEQRES 8 B 200 ARG SER TYR TYR ARG GLY ALA ALA GLY ALA LEU LEU VAL SEQRES 9 B 200 TYR ASP ILE THR SER ARG GLU THR TYR ASN SER LEU ALA SEQRES 10 B 200 ALA TRP LEU THR ASP ALA ARG THR LEU ALA SER PRO ASN SEQRES 11 B 200 ILE VAL VAL ILE LEU CYS GLY ASN LYS LYS ASP LEU ASP SEQRES 12 B 200 PRO GLU ARG GLU VAL THR PHE LEU GLU ALA SER ARG PHE SEQRES 13 B 200 ALA GLN GLU ASN GLU LEU MET PHE LEU GLU THR SER ALA SEQRES 14 B 200 LEU THR GLY GLU ASN VAL GLU GLU ALA PHE LEU LYS CYS SEQRES 15 B 200 ALA ARG THR ILE LEU ASN LYS ILE ASP SER GLY GLU LEU SEQRES 16 B 200 ASP PRO GLU ARG MET HET MG A 602 1 HET GDP A 601 28 HET BME A 603 2 HET UNX A1003 1 HET MG B 602 1 HET GDP B 601 28 HET BME B 603 2 HETNAM MG MAGNESIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM BME BETA-MERCAPTOETHANOL HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 MG 2(MG 2+) FORMUL 4 GDP 2(C10 H15 N5 O11 P2) FORMUL 5 BME 2(C2 H6 O S) FORMUL 6 UNX X FORMUL 10 HOH *75(H2 O) HELIX 1 1 GLY A 20 GLU A 30 1 11 HELIX 2 2 GLY A 66 ARG A 71 1 6 HELIX 3 3 THR A 74 ARG A 79 1 6 HELIX 4 4 SER A 92 SER A 98 1 7 HELIX 5 5 SER A 98 ALA A 110 1 13 HELIX 6 6 LYS A 123 ARG A 129 5 7 HELIX 7 7 THR A 132 ASN A 143 1 12 HELIX 8 8 ASN A 157 SER A 175 1 19 HELIX 9 9 ASP A 179 MET A 183 5 5 HELIX 10 10 GLY B 20 GLU B 30 1 11 HELIX 11 11 GLY B 66 PHE B 70 5 5 HELIX 12 12 THR B 74 ARG B 79 1 6 HELIX 13 13 SER B 92 SER B 98 1 7 HELIX 14 14 SER B 98 ALA B 110 1 13 HELIX 15 15 LYS B 122 ARG B 129 5 8 HELIX 16 16 THR B 132 ASN B 143 1 12 HELIX 17 17 ASN B 157 ILE B 173 1 17 SHEET 1 A 6 PHE A 45 VAL A 52 0 SHEET 2 A 6 LYS A 55 TRP A 62 -1 O ILE A 61 N GLY A 46 SHEET 3 A 6 PHE A 7 GLY A 15 1 N PHE A 7 O LYS A 58 SHEET 4 A 6 GLY A 83 ASP A 89 1 O VAL A 87 N ILE A 14 SHEET 5 A 6 VAL A 115 ASN A 121 1 O ASN A 121 N TYR A 88 SHEET 6 A 6 MET A 146 THR A 150 1 O MET A 146 N LEU A 118 SHEET 1 B 6 PHE B 45 VAL B 52 0 SHEET 2 B 6 LYS B 55 TRP B 62 -1 O ILE B 61 N GLY B 46 SHEET 3 B 6 PHE B 7 ILE B 14 1 N PHE B 9 O LYS B 58 SHEET 4 B 6 GLY B 83 ASP B 89 1 O VAL B 87 N ILE B 14 SHEET 5 B 6 VAL B 115 ASN B 121 1 O ILE B 117 N LEU B 86 SHEET 6 B 6 MET B 146 GLU B 149 1 O MET B 146 N LEU B 118 LINK OG SER A 22 MG MG A 602 1555 1555 2.17 LINK O2B GDP A 601 MG MG A 602 1555 1555 2.16 LINK MG MG A 602 O HOH A1004 1555 1555 2.07 LINK MG MG A 602 O HOH A1005 1555 1555 2.02 LINK MG MG A 602 O HOH A1006 1555 1555 2.15 LINK MG MG A 602 O HOH A1007 1555 1555 2.11 LINK OG SER B 22 MG MG B 602 1555 1555 2.16 LINK O2B GDP B 601 MG MG B 602 1555 1555 2.16 LINK MG MG B 602 O HOH B 604 1555 1555 2.08 LINK MG MG B 602 O HOH B 605 1555 1555 2.17 LINK MG MG B 602 O HOH B 606 1555 1555 2.22 LINK MG MG B 602 O HOH B 607 1555 1555 2.25 SITE 1 AC1 6 SER A 22 GDP A 601 HOH A1004 HOH A1005 SITE 2 AC1 6 HOH A1006 HOH A1007 SITE 1 AC2 6 SER B 22 GDP B 601 HOH B 604 HOH B 605 SITE 2 AC2 6 HOH B 606 HOH B 607 SITE 1 AC3 18 SER A 16 GLY A 18 THR A 19 GLY A 20 SITE 2 AC3 18 LYS A 21 SER A 22 CYS A 23 ASN A 121 SITE 3 AC3 18 LYS A 122 ASP A 124 LEU A 125 SER A 151 SITE 4 AC3 18 ALA A 152 LEU A 153 MG A 602 HOH A1005 SITE 5 AC3 18 HOH A1006 HOH A1007 SITE 1 AC4 2 CYS A 23 LEU A 153 SITE 1 AC5 22 GLY A 53 GLY A 54 LYS A 55 SER B 16 SITE 2 AC5 22 GLY B 18 THR B 19 GLY B 20 LYS B 21 SITE 3 AC5 22 SER B 22 CYS B 23 ARG B 69 ASN B 121 SITE 4 AC5 22 LYS B 122 ASP B 124 LEU B 125 SER B 151 SITE 5 AC5 22 ALA B 152 LEU B 153 MG B 602 BME B 603 SITE 6 AC5 22 HOH B 604 HOH B 606 SITE 1 AC6 2 CYS B 23 GDP B 601 SITE 1 AC7 2 HOH A1023 ASN B 157 CRYST1 67.528 67.528 179.955 90.00 90.00 90.00 P 43 21 2 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 0.014810 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014810 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005560 0.00000