10 20 30 40 50 60 70 80 1ZBD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER G PROTEIN 06-NOV-98 1ZBD
TITLE STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: CRYSTAL TITLE 2 STRUCTURE OF THE SMALL G PROTEIN RAB3A COMPLEXED WITH THE TITLE 3 EFFECTOR DOMAIN OF RABPHILIN-3A
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RABPHILIN-3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 19-217; COMPND 5 SYNONYM: RAS-RELATED PROTEIN RAB-3A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RABPHILIN-3A; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: 40-170, EFFECTOR DOMAIN; COMPND 12 SYNONYM: RAS-RELATED PROTEIN RAB-3A; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: COMPLEXED WITH GUANOSINE-5'-TRIPHOSPHATE
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGAN: BRAIN; SOURCE 6 TISSUE: NEURONS; SOURCE 7 CELLULAR_LOCATION: SYNAPTIC VESICLES; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 11 EXPRESSION_SYSTEM_VARIANT: (DE3); SOURCE 12 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 14 MOL_ID: 2; SOURCE 15 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 16 ORGANISM_COMMON: NORWAY RAT; SOURCE 17 ORGANISM_TAXID: 10116; SOURCE 18 ORGAN: BRAIN; SOURCE 19 TISSUE: NEURONS; SOURCE 20 CELLULAR_LOCATION: SYNAPTIC VESICLES; SOURCE 21 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 22 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 23 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 24 EXPRESSION_SYSTEM_VARIANT: (DE3); SOURCE 25 EXPRESSION_SYSTEM_CELLULAR_LOCATION: CYTOPLASM; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS G PROTEIN, EFFECTOR, RABCDR, SYNAPTIC EXOCYTOSIS, RAB KEYWDS 2 PROTEIN, RAB3A, RABPHILIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.OSTERMEIER,A.T.BRUNGER
REVDAT 2 24-FEB-09 1ZBD 1 VERSN REVDAT 1 02-APR-99 1ZBD 0
JRNL AUTH C.OSTERMEIER,A.T.BRUNGER JRNL TITL STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY: JRNL TITL 2 CRYSTAL STRUCTURE OF THE SMALL G PROTEIN RAB3A JRNL TITL 3 COMPLEXED WITH THE EFFECTOR DOMAIN OF RABPHILIN-3A. JRNL REF CELL(CAMBRIDGE,MASS.) V. 96 363 1999 JRNL REFN ISSN 0092-8674 JRNL PMID 10025402 JRNL DOI 10.1016/S0092-8674(00)80549-8
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.4 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 23478 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 SET) : 0.226 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2213 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3456 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 336 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2445 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 46 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.16000 REMARK 3 B22 (A**2) : 1.18000 REMARK 3 B33 (A**2) : -7.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.43 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.44 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.89 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 6.520 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 8.800 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 9.850 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 12.390; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 49.72 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : GTP.PAR REMARK 3 PARAMETER FILE 4 : WATER.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1ZBD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789, 0.9793, 0.9879 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23889 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.04900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.22000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: CNS 0.4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0
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 44.65750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.80950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.65750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.80950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC 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: 16030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 89.31500 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 15 REMARK 465 THR A 193 REMARK 465 ALA A 194 REMARK 465 ASP A 195 REMARK 465 PRO A 196 REMARK 465 ALA A 197 REMARK 465 VAL A 198 REMARK 465 THR A 199 REMARK 465 GLY A 200 REMARK 465 ALA A 201 REMARK 465 LYS A 202 REMARK 465 GLN A 203 REMARK 465 GLY A 204 REMARK 465 PRO A 205 REMARK 465 GLN A 206 REMARK 465 LEU A 207 REMARK 465 THR A 208 REMARK 465 ASP A 209 REMARK 465 GLN A 210 REMARK 465 GLN A 211 REMARK 465 ALA A 212 REMARK 465 PRO A 213 REMARK 465 PRO A 214 REMARK 465 HIS A 215 REMARK 465 GLN A 216 REMARK 465 ASP A 217 REMARK 465 GLY B 37 REMARK 465 SER B 38 REMARK 465 HIS B 39 REMARK 465 MSE B 40 REMARK 465 ARG B 41 REMARK 465 LYS B 42 REMARK 465 GLN B 43 REMARK 465 PRO B 168 REMARK 465 ILE B 169 REMARK 465 LYS B 170
REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 PHE A 47 CG CD1 CD2 CE1 CE2 CZ REMARK 480 ASP A 68 OD1 OD2 REMARK 480 GLU A 148 CG CD OE1 OE2 REMARK 480 ASP A 192 OD1 OD2 REMARK 480 ASP B 48 OD1 OD2 REMARK 480 ARG B 93 NE CZ NH1 NH2 REMARK 480 ARG B 130 NE CZ NH1 NH2 REMARK 480 HIS B 132 CG ND1 CD2 CE1 NE2 REMARK 480 LYS B 160 CG CD CE NZ REMARK 480 GLN B 161 CB CG CD OE1 NE2 REMARK 480 MSE B 167 CB CG SE CE
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 CD1 LEU B 46 CD1 LEU B 46 2556 2.12 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 32 -0.09 76.32 REMARK 500 ALA A 43 -70.81 -76.39 REMARK 500 PRO A 49 -15.64 -46.20 REMARK 500 LYS A 136 34.31 72.45 REMARK 500 ASN A 169 66.08 20.56 REMARK 500 ASN A 171 15.08 57.23 REMARK 500 THR B 47 106.02 -163.83 REMARK 500 ASP B 48 -108.98 -59.73 REMARK 500 VAL B 91 -82.06 -99.34 REMARK 500 CYS B 94 140.04 -34.26 REMARK 500 LEU B 96 -74.13 -82.15 REMARK 500 ASN B 128 -133.94 -117.73 REMARK 500 ASN B 129 50.93 -110.11 REMARK 500 PRO B 131 172.22 -51.80 REMARK 500 LEU B 163 78.09 -114.43 REMARK 500 PRO B 164 176.01 -57.87 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 36 OG1 REMARK 620 2 THR A 54 OG1 79.6 REMARK 620 3 GTP A 303 O3G 134.1 74.5 REMARK 620 4 GTP A 303 O2B 86.0 131.4 83.7 REMARK 620 5 GTP A 303 O3B 138.4 128.8 54.5 52.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 114 SG REMARK 620 2 CYS B 137 SG 120.1 REMARK 620 3 CYS B 111 SG 104.5 115.9 REMARK 620 4 CYS B 140 SG 112.1 92.5 111.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 119 SG REMARK 620 2 CYS B 94 SG 103.0 REMARK 620 3 CYS B 97 SG 128.4 99.0 REMARK 620 4 CYS B 122 SG 103.2 104.0 115.8 REMARK 620 N 1 2 3
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: ZN1 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN-BINDING RESIDUES FOR ZN 301 REMARK 800 SITE_IDENTIFIER: ZN2 REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: ZN-BINDING RESIDUES FOR ZN 300 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 300 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GTP A 303
DBREF 1ZBD A 19 217 UNP P63012 RAB3A_RAT 19 217 DBREF 1ZBD B 41 170 UNP P47709 RP3A_RAT 41 170
SEQADV 1ZBD MSE A 22 UNP P63012 MET 22 CONFLICT SEQADV 1ZBD LEU A 81 UNP P63012 GLN 81 SEE REMARK 999 SEQADV 1ZBD MSE A 96 UNP P63012 MET 96 CONFLICT SEQADV 1ZBD MSE A 101 UNP P63012 MET 101 CONFLICT SEQADV 1ZBD MSE A 139 UNP P63012 MET 139 CONFLICT SEQADV 1ZBD MSE A 187 UNP P63012 MET 187 CONFLICT SEQADV 1ZBD MSE B 64 UNP P47709 MET 64 CONFLICT SEQADV 1ZBD MSE B 67 UNP P47709 MET 67 CONFLICT SEQADV 1ZBD MSE B 82 UNP P47709 MET 82 CONFLICT SEQADV 1ZBD MSE B 103 UNP P47709 MET 103 CONFLICT SEQADV 1ZBD SER B 108 UNP P47709 CYS 108 SEE REMARK 999 SEQADV 1ZBD MSE B 167 UNP P47709 MET 167 CONFLICT
SEQRES 1 A 203 GLY SER HIS MSE PHE ASP TYR MSE PHE LYS ILE LEU ILE SEQRES 2 A 203 ILE GLY ASN SER SER VAL GLY LYS THR SER PHE LEU PHE SEQRES 3 A 203 ARG TYR ALA ASP ASP SER PHE THR PRO ALA PHE VAL SER SEQRES 4 A 203 THR VAL GLY ILE ASP PHE LYS VAL LYS THR ILE TYR ARG SEQRES 5 A 203 ASN ASP LYS ARG ILE LYS LEU GLN ILE TRP ASP THR ALA SEQRES 6 A 203 GLY LEU GLU ARG TYR ARG THR ILE THR THR ALA TYR TYR SEQRES 7 A 203 ARG GLY ALA MSE GLY PHE ILE LEU MSE TYR ASP ILE THR SEQRES 8 A 203 ASN GLU GLU SER PHE ASN ALA VAL GLN ASP TRP SER THR SEQRES 9 A 203 GLN ILE LYS THR TYR SER TRP ASP ASN ALA GLN VAL LEU SEQRES 10 A 203 LEU VAL GLY ASN LYS CYS ASP MSE GLU ASP GLU ARG VAL SEQRES 11 A 203 VAL SER SER GLU ARG GLY ARG GLN LEU ALA ASP HIS LEU SEQRES 12 A 203 GLY PHE GLU PHE PHE GLU ALA SER ALA LYS ASP ASN ILE SEQRES 13 A 203 ASN VAL LYS GLN THR PHE GLU ARG LEU VAL ASP VAL ILE SEQRES 14 A 203 CYS GLU LYS MSE SER GLU SER LEU ASP THR ALA ASP PRO SEQRES 15 A 203 ALA VAL THR GLY ALA LYS GLN GLY PRO GLN LEU THR ASP SEQRES 16 A 203 GLN GLN ALA PRO PRO HIS GLN ASP SEQRES 1 B 134 GLY SER HIS MSE ARG LYS GLN GLU GLU LEU THR ASP GLU SEQRES 2 B 134 GLU LYS GLU ILE ILE ASN ARG VAL ILE ALA ARG ALA GLU SEQRES 3 B 134 LYS MSE GLU THR MSE GLU GLN GLU ARG ILE GLY ARG LEU SEQRES 4 B 134 VAL ASP ARG LEU GLU THR MSE ARG LYS ASN VAL ALA GLY SEQRES 5 B 134 ASP GLY VAL ASN ARG CYS ILE LEU CYS GLY GLU GLN LEU SEQRES 6 B 134 GLY MSE LEU GLY SER ALA SER VAL VAL CYS GLU ASP CYS SEQRES 7 B 134 LYS LYS ASN VAL CYS THR LYS CYS GLY VAL GLU THR SER SEQRES 8 B 134 ASN ASN ARG PRO HIS PRO VAL TRP LEU CYS LYS ILE CYS SEQRES 9 B 134 LEU GLU GLN ARG GLU VAL TRP LYS ARG SER GLY ALA TRP SEQRES 10 B 134 PHE PHE LYS GLY PHE PRO LYS GLN VAL LEU PRO GLN PRO SEQRES 11 B 134 MSE PRO ILE LYS
MODRES 1ZBD MSE A 18 MET SELENOMETHIONINE MODRES 1ZBD MSE A 22 MET SELENOMETHIONINE MODRES 1ZBD MSE A 96 MET SELENOMETHIONINE MODRES 1ZBD MSE A 101 MET SELENOMETHIONINE MODRES 1ZBD MSE A 139 MET SELENOMETHIONINE MODRES 1ZBD MSE A 187 MET SELENOMETHIONINE MODRES 1ZBD MSE B 64 MET SELENOMETHIONINE MODRES 1ZBD MSE B 67 MET SELENOMETHIONINE MODRES 1ZBD MSE B 82 MET SELENOMETHIONINE MODRES 1ZBD MSE B 103 MET SELENOMETHIONINE MODRES 1ZBD MSE B 167 MET SELENOMETHIONINE
HET MSE A 18 8 HET MSE A 22 8 HET MSE A 96 8 HET MSE A 101 8 HET MSE A 139 8 HET MSE A 187 8 HET MSE B 64 8 HET MSE B 67 8 HET MSE B 82 8 HET MSE B 103 8 HET MSE B 167 8 HET ZN B 300 1 HET ZN B 301 1 HET MG A 302 1 HET GTP A 303 32
HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE
FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 3 ZN 2(ZN 2+) FORMUL 5 MG MG 2+ FORMUL 6 GTP C10 H16 N5 O14 P3 FORMUL 7 HOH *46(H2 O)
HELIX 1 1 LYS A 35 ALA A 43 1 9 HELIX 2 2 GLU A 82 GLY A 94 5 13 HELIX 3 3 GLU A 107 TYR A 123 1 17 HELIX 4 4 SER A 147 LEU A 157 1 11 HELIX 5 5 LYS A 173 SER A 190 1 18 HELIX 6 6 GLU B 50 ASN B 85 1 36 HELIX 7 7 LYS B 138 ARG B 149 1 12 HELIX 8 8 ALA B 152 PHE B 155 1 4
SHEET 1 A 6 GLU A 160 ALA A 164 0 SHEET 2 A 6 VAL A 130 ASN A 135 1 N LEU A 132 O GLU A 160 SHEET 3 A 6 GLY A 97 LEU A 100 1 N PHE A 98 O LEU A 131 SHEET 4 A 6 LYS A 24 ILE A 27 1 N LEU A 26 O GLY A 97 SHEET 5 A 6 LYS A 69 THR A 78 1 N GLN A 74 O ILE A 25 SHEET 6 A 6 ILE A 57 ARG A 66 -1 N ARG A 66 O LYS A 69 SHEET 1 B 2 SER B 108 VAL B 110 0 SHEET 2 B 2 ASN B 117 CYS B 119 -1 N VAL B 118 O VAL B 109 SHEET 1 C 2 GLY B 123 GLU B 125 0 SHEET 2 C 2 TRP B 135 CYS B 137 -1 N LEU B 136 O VAL B 124
LINK N MSE A 18 C HIS A 17 1555 1555 1.33 LINK C MSE A 18 N PHE A 19 1555 1555 1.33 LINK N MSE A 22 C TYR A 21 1555 1555 1.32 LINK C MSE A 22 N PHE A 23 1555 1555 1.33 LINK N MSE A 96 C ALA A 95 1555 1555 1.33 LINK C MSE A 96 N GLY A 97 1555 1555 1.33 LINK N MSE A 101 C LEU A 100 1555 1555 1.33 LINK C MSE A 101 N TYR A 102 1555 1555 1.33 LINK N MSE A 139 C ASP A 138 1555 1555 1.33 LINK C MSE A 139 N GLU A 140 1555 1555 1.33 LINK N MSE A 187 C LYS A 186 1555 1555 1.33 LINK C MSE A 187 N SER A 188 1555 1555 1.32 LINK N MSE B 64 C LYS B 63 1555 1555 1.33 LINK C MSE B 64 N GLU B 65 1555 1555 1.33 LINK N MSE B 67 C THR B 66 1555 1555 1.33 LINK C MSE B 67 N GLU B 68 1555 1555 1.33 LINK N MSE B 82 C THR B 81 1555 1555 1.33 LINK C MSE B 82 N ARG B 83 1555 1555 1.33 LINK N MSE B 103 C GLY B 102 1555 1555 1.33 LINK C MSE B 103 N LEU B 104 1555 1555 1.33 LINK N MSE B 167 C PRO B 166 1555 1555 1.33 LINK MG MG A 302 OG1 THR A 36 1555 1555 2.34 LINK MG MG A 302 OG1 THR A 54 1555 1555 2.44 LINK MG MG A 302 O3G GTP A 303 1555 1555 2.42 LINK MG MG A 302 O2B GTP A 303 1555 1555 2.59 LINK MG MG A 302 O3B GTP A 303 1555 1555 3.10 LINK ZN ZN B 300 SG CYS B 114 1555 1555 2.64 LINK ZN ZN B 300 SG CYS B 137 1555 1555 2.67 LINK ZN ZN B 300 SG CYS B 111 1555 1555 2.52 LINK ZN ZN B 300 SG CYS B 140 1555 1555 2.54 LINK ZN ZN B 301 SG CYS B 119 1555 1555 2.63 LINK SG CYS B 94 ZN ZN B 301 1555 1555 2.79 LINK SG CYS B 97 ZN ZN B 301 1555 1555 2.83 LINK SG CYS B 122 ZN ZN B 301 1555 1555 2.84
SITE 1 ZN1 4 CYS B 94 CYS B 97 CYS B 119 CYS B 122 SITE 1 ZN2 4 CYS B 111 CYS B 114 CYS B 137 CYS B 140 SITE 1 AC1 4 CYS B 111 CYS B 114 CYS B 137 CYS B 140 SITE 1 AC2 4 CYS B 94 CYS B 97 CYS B 119 CYS B 122 SITE 1 AC3 3 THR A 36 THR A 54 GTP A 303 SITE 1 AC4 23 ASN A 30 SER A 31 SER A 32 VAL A 33 SITE 2 AC4 23 GLY A 34 LYS A 35 THR A 36 SER A 37 SITE 3 AC4 23 THR A 48 PRO A 49 ALA A 50 PHE A 51 SITE 4 AC4 23 SER A 53 THR A 54 GLY A 80 ASN A 135 SITE 5 AC4 23 LYS A 136 ASP A 138 MSE A 139 SER A 165 SITE 6 AC4 23 ALA A 166 LYS A 167 MG A 302
CRYST1 89.315 95.619 47.715 90.00 94.49 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 0.011196 0.000000 0.000879 0.00000
SCALE2 0.000000 0.010458 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021022 0.00000