PDB Short entry for 3DZ8 HEADER PROTEIN TRANSPORT 29-JUL-08 3DZ8 TITLE CRYSTAL STRUCTURE OF HUMAN RAB3B GTPASE BOUND WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-3B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 18-190; 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: RAB3B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-V2R; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL (GI:134105571) KEYWDS RAS, GDP, GTPASE, STRUCTURAL GENOMICS CONSORTIUM, SGC, CELL MEMBRANE, KEYWDS 2 GTP-BINDING, LIPOPROTEIN, MEMBRANE, METHYLATION, NUCLEOTIDE-BINDING, KEYWDS 3 PHOSPHOPROTEIN, PRENYLATION, PROTEIN TRANSPORT, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.SHEN,Y.TONG,D.SUKUMAR,W.TEMPEL,P.LOPPNAU,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,C.BOUNTRA,M.WILKSTROM,A.BOCHKAREV,H.PARK,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 5 30-AUG-23 3DZ8 1 REMARK SEQADV REVDAT 4 25-OCT-17 3DZ8 1 REMARK REVDAT 3 13-JUL-11 3DZ8 1 VERSN REVDAT 2 24-FEB-09 3DZ8 1 VERSN REVDAT 1 12-AUG-08 3DZ8 0 JRNL AUTH Y.SHEN,Y.TONG,D.SUKUMAR,W.TEMPEL,P.LOPPNAU,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,C.BOUNTRA,M.WILKSTROM,A.BOCHKAREV,H.PARK JRNL TITL CRYSTAL STRUCTURE OF HUMAN RAB3B GTPASE BOUND WITH GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0044 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) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15562 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.903 REMARK 3 FREE R VALUE TEST SET COUNT : 763 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) : 1037 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.48 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 47 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1390 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 30 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) : 15.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.20800 REMARK 3 B22 (A**2) : 1.53700 REMARK 3 B33 (A**2) : -1.46400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.566 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1456 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 962 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1976 ; 1.381 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2330 ; 0.862 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 179 ; 6.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 66 ;38.192 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 240 ;12.066 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;16.515 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 221 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1618 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 324 ; 0.001 ; 0.020 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): 884 ; 1.403 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 364 ; 0.415 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1419 ; 2.134 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 572 ; 1.684 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 556 ; 2.368 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 10 A 187 REMARK 3 ORIGIN FOR THE GROUP (A): 14.0635 7.9495 19.0319 REMARK 3 T TENSOR REMARK 3 T11: 0.0998 T22: 0.1620 REMARK 3 T33: 0.1222 T12: -0.0017 REMARK 3 T13: 0.0118 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 2.2491 L22: 0.9063 REMARK 3 L33: 3.9417 L12: -0.2879 REMARK 3 L13: 1.0967 L23: -0.2367 REMARK 3 S TENSOR REMARK 3 S11: 0.0117 S12: 0.5953 S13: 0.0624 REMARK 3 S21: -0.1411 S22: -0.0209 S23: -0.1674 REMARK 3 S31: 0.1075 S32: 0.2952 S33: 0.0091 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 201 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): 0.1834 6.3456 16.9318 REMARK 3 T TENSOR REMARK 3 T11: 0.0583 T22: 0.1148 REMARK 3 T33: 0.0726 T12: -0.0124 REMARK 3 T13: -0.0313 T23: -0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.6703 L22: 6.8177 REMARK 3 L33: 10.1764 L12: -0.5362 REMARK 3 L13: 1.5328 L23: 5.6964 REMARK 3 S TENSOR REMARK 3 S11: 0.0801 S12: 0.1975 S13: -0.1697 REMARK 3 S21: 0.1134 S22: -0.2703 S23: 0.4493 REMARK 3 S31: 0.2552 S32: -0.6368 S33: 0.1902 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: REMARK 3 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. HYDROGENS HAVE BEEN REMARK 3 ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3DZ8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048674. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 DW 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 : 15627 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 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 2GF9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2M AMMONIUM SULFATE, 0.2M SODIUM REMARK 280 ACETATE, 0.1M HEPES, 5% MPD, PH 7.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 28.48450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.43750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 28.48450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.43750 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 30.71786 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 68.70896 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 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 SER A 188 REMARK 465 ASP A 189 REMARK 465 SER A 190 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 TYR A 21 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A 47 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 68 CG CD OE1 OE2 REMARK 470 LYS A 69 CE NZ REMARK 470 ARG A 85 CD NE CZ NH1 NH2 REMARK 470 GLU A 108 CD OE1 OE2 REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 TYR A 123 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 ASN A 127 CG OD1 ND2 REMARK 470 GLU A 142 CD OE1 OE2 REMARK 470 GLU A 148 CG CD OE1 OE2 REMARK 470 GLU A 155 CD OE1 OE2 REMARK 470 PHE A 162 CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 167 CD CE NZ REMARK 470 ARG A 178 CD NE CZ NH1 NH2 REMARK 470 ASP A 185 CG OD1 OD2 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 32 8.43 82.26 REMARK 500 ASP A 58 24.51 -152.76 REMARK 500 LYS A 136 31.26 74.96 REMARK 500 MET A 139 54.11 -96.20 REMARK 500 REMARK 500 REMARK: NULL 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 505 DBREF 3DZ8 A 18 190 UNP P20337 RAB3B_HUMAN 18 190 SEQADV 3DZ8 MET A 0 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 1 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 2 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 3 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 4 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 5 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 HIS A 6 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 SER A 7 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 SER A 8 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 GLY A 9 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 ARG A 10 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 GLU A 11 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 ASN A 12 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 LEU A 13 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 TYR A 14 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 PHE A 15 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 GLN A 16 UNP P20337 EXPRESSION TAG SEQADV 3DZ8 GLY A 17 UNP P20337 EXPRESSION TAG SEQRES 1 A 191 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 191 LEU TYR PHE GLN GLY ASN PHE ASP TYR MET PHE LYS LEU SEQRES 3 A 191 LEU ILE ILE GLY ASN SER SER VAL GLY LYS THR SER PHE SEQRES 4 A 191 LEU PHE ARG TYR ALA ASP ASP THR PHE THR PRO ALA PHE SEQRES 5 A 191 VAL SER THR VAL GLY ILE ASP PHE LYS VAL LYS THR VAL SEQRES 6 A 191 TYR ARG HIS GLU LYS ARG VAL LYS LEU GLN ILE TRP ASP SEQRES 7 A 191 THR ALA GLY GLN GLU ARG TYR ARG THR ILE THR THR ALA SEQRES 8 A 191 TYR TYR ARG GLY ALA MET GLY PHE ILE LEU MET TYR ASP SEQRES 9 A 191 ILE THR ASN GLU GLU SER PHE ASN ALA VAL GLN ASP TRP SEQRES 10 A 191 ALA THR GLN ILE LYS THR TYR SER TRP ASP ASN ALA GLN SEQRES 11 A 191 VAL ILE LEU VAL GLY ASN LYS CYS ASP MET GLU GLU GLU SEQRES 12 A 191 ARG VAL VAL PRO THR GLU LYS GLY GLN LEU LEU ALA GLU SEQRES 13 A 191 GLN LEU GLY PHE ASP PHE PHE GLU ALA SER ALA LYS GLU SEQRES 14 A 191 ASN ILE SER VAL ARG GLN ALA PHE GLU ARG LEU VAL ASP SEQRES 15 A 191 ALA ILE CYS ASP LYS MET SER ASP SER HET GDP A 201 28 HET UNX A 501 1 HET UNX A 502 1 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 UNX 6(X) FORMUL 9 HOH *30(H2 O) HELIX 1 1 GLY A 34 THR A 46 1 13 HELIX 2 2 ASP A 77 TYR A 84 1 8 HELIX 3 3 TYR A 84 ARG A 93 1 10 HELIX 4 4 ASN A 106 ALA A 112 1 7 HELIX 5 5 ALA A 112 SER A 124 1 13 HELIX 6 6 MET A 139 ARG A 143 5 5 HELIX 7 7 PRO A 146 GLY A 158 1 13 HELIX 8 8 SER A 171 MET A 187 1 17 SHEET 1 A 2 ASN A 12 PHE A 15 0 SHEET 2 A 2 ASN A 18 TYR A 21 -1 O ASP A 20 N LEU A 13 SHEET 1 B 7 PHE A 51 VAL A 55 0 SHEET 2 B 7 PHE A 59 ARG A 66 -1 O PHE A 59 N VAL A 55 SHEET 3 B 7 VAL A 71 TRP A 76 -1 O LEU A 73 N VAL A 64 SHEET 4 B 7 PHE A 23 GLY A 29 1 N LEU A 25 O LYS A 72 SHEET 5 B 7 GLY A 97 ASP A 103 1 O MET A 101 N ILE A 28 SHEET 6 B 7 GLN A 129 ASN A 135 1 O ASN A 135 N TYR A 102 SHEET 7 B 7 ASP A 160 GLU A 163 1 O ASP A 160 N LEU A 132 SITE 1 AC1 15 SER A 32 GLY A 34 LYS A 35 THR A 36 SITE 2 AC1 15 SER A 37 ASN A 135 LYS A 136 ASP A 138 SITE 3 AC1 15 MET A 139 SER A 165 ALA A 166 LYS A 167 SITE 4 AC1 15 HOH A 511 HOH A 520 HOH A 522 SITE 1 AC2 3 SER A 31 ALA A 79 HOH A 510 SITE 1 AC3 5 PHE A 15 GLN A 16 ALA A 43 ASP A 44 SITE 2 AC3 5 THR A 48 SITE 1 AC4 2 ARG A 66 ARG A 173 SITE 1 AC5 2 ASN A 169 ARG A 173 CRYST1 56.969 50.875 73.553 90.00 110.91 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017553 0.000000 0.006708 0.00000 SCALE2 0.000000 0.019656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014554 0.00000