HEADER STRUCTURAL GENOMICS 29-FEB-20 6Y7G TITLE STRUCTURE OF THE HUMAN RAB3C IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-3C; 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: RAB3C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A-LIC KEYWDS RAB3C, HUMAN RAS-RELATED PROTEIN RAB-3C, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR L.DIAZ-SAEZ,S.JUNG,B.RAUX,N.A.BURGESS-BROWN,F.VON DELFT, AUTHOR 2 C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,K.V.M.HUBER,STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (SGC) REVDAT 2 24-JAN-24 6Y7G 1 REMARK REVDAT 1 31-MAR-21 6Y7G 0 JRNL AUTH L.DIAZ-SAEZ,S.JUNG,N.A.BURGESS-BROWN,F.VON DELFT, JRNL AUTH 2 C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,K.V.M.HUBER JRNL TITL STRUCTURE OF THE HUMAN RAB3C IN COMPLEX WITH GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 15301 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 792 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1146 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 57 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2655 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 82 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.44000 REMARK 3 B22 (A**2) : 1.66000 REMARK 3 B33 (A**2) : -1.01000 REMARK 3 B12 (A**2) : -0.31000 REMARK 3 B13 (A**2) : 0.15000 REMARK 3 B23 (A**2) : -2.27000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.395 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.293 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.242 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.340 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.867 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2797 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2478 ; 0.003 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3782 ; 1.498 ; 1.677 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5761 ; 1.204 ; 1.596 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 336 ; 7.151 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;36.175 ;23.938 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 489 ;16.064 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;10.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.062 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3096 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 619 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6Y7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292107040. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16096 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 63.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.57300 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 2.8.3 REMARK 200 STARTING MODEL: 1ZBD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M BIS-TRIS PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 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 1 REMARK 465 ARG A 2 REMARK 465 HIS A 3 REMARK 465 GLU A 4 REMARK 465 ALA A 5 REMARK 465 PRO A 6 REMARK 465 MET A 7 REMARK 465 GLN A 8 REMARK 465 MET A 9 REMARK 465 ALA A 10 REMARK 465 SER A 11 REMARK 465 ALA A 12 REMARK 465 GLN A 13 REMARK 465 ASP A 14 REMARK 465 ALA A 15 REMARK 465 ARG A 16 REMARK 465 TYR A 17 REMARK 465 GLY A 18 REMARK 465 GLN A 19 REMARK 465 LYS A 20 REMARK 465 ASP A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 ASP A 24 REMARK 465 PHE A 59 REMARK 465 VAL A 60 REMARK 465 SER A 61 REMARK 465 THR A 62 REMARK 465 VAL A 63 REMARK 465 GLU A 90 REMARK 465 ARG A 91 REMARK 465 TYR A 92 REMARK 465 ARG A 93 REMARK 465 THR A 94 REMARK 465 ILE A 95 REMARK 465 THR A 96 REMARK 465 THR A 97 REMARK 465 ALA A 98 REMARK 465 SER A 198 REMARK 465 LEU A 199 REMARK 465 GLU A 200 REMARK 465 THR A 201 REMARK 465 ASP A 202 REMARK 465 PRO A 203 REMARK 465 ALA A 204 REMARK 465 ILE A 205 REMARK 465 THR A 206 REMARK 465 ALA A 207 REMARK 465 ALA A 208 REMARK 465 LYS A 209 REMARK 465 GLN A 210 REMARK 465 ASN A 211 REMARK 465 THR A 212 REMARK 465 ARG A 213 REMARK 465 LEU A 214 REMARK 465 LYS A 215 REMARK 465 GLU A 216 REMARK 465 THR A 217 REMARK 465 PRO A 218 REMARK 465 PRO A 219 REMARK 465 PRO A 220 REMARK 465 PRO A 221 REMARK 465 GLN A 222 REMARK 465 PRO A 223 REMARK 465 ASN A 224 REMARK 465 CYS A 225 REMARK 465 ALA A 226 REMARK 465 CYS A 227 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 HIS B 3 REMARK 465 GLU B 4 REMARK 465 ALA B 5 REMARK 465 PRO B 6 REMARK 465 MET B 7 REMARK 465 GLN B 8 REMARK 465 MET B 9 REMARK 465 ALA B 10 REMARK 465 SER B 11 REMARK 465 ALA B 12 REMARK 465 GLN B 13 REMARK 465 ASP B 14 REMARK 465 ALA B 15 REMARK 465 ARG B 16 REMARK 465 TYR B 17 REMARK 465 GLY B 18 REMARK 465 GLN B 19 REMARK 465 LYS B 20 REMARK 465 ASP B 21 REMARK 465 SER B 22 REMARK 465 SER B 23 REMARK 465 ASP B 24 REMARK 465 GLN B 25 REMARK 465 SER B 57 REMARK 465 ALA B 58 REMARK 465 PHE B 59 REMARK 465 VAL B 60 REMARK 465 SER B 61 REMARK 465 THR B 62 REMARK 465 VAL B 63 REMARK 465 SER B 198 REMARK 465 LEU B 199 REMARK 465 GLU B 200 REMARK 465 THR B 201 REMARK 465 ASP B 202 REMARK 465 PRO B 203 REMARK 465 ALA B 204 REMARK 465 ILE B 205 REMARK 465 THR B 206 REMARK 465 ALA B 207 REMARK 465 ALA B 208 REMARK 465 LYS B 209 REMARK 465 GLN B 210 REMARK 465 ASN B 211 REMARK 465 THR B 212 REMARK 465 ARG B 213 REMARK 465 LEU B 214 REMARK 465 LYS B 215 REMARK 465 GLU B 216 REMARK 465 THR B 217 REMARK 465 PRO B 218 REMARK 465 PRO B 219 REMARK 465 PRO B 220 REMARK 465 PRO B 221 REMARK 465 GLN B 222 REMARK 465 PRO B 223 REMARK 465 ASN B 224 REMARK 465 CYS B 225 REMARK 465 ALA B 226 REMARK 465 CYS B 227 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 GLN A 25 CB CG CD OE1 NE2 REMARK 480 TYR A 99 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR A 99 OH REMARK 480 ARG A 101 CB CG CD NE CZ NH1 NH2 REMARK 480 TYR A 131 CG CD1 CD2 CE1 CE2 CZ OH REMARK 480 LYS A 181 CG CD CE NZ REMARK 480 ASN B 26 CB CG OD1 ND2 REMARK 480 ASP B 134 CB CG OD1 OD2 REMARK 480 ASN B 135 CB CG OD1 ND2 REMARK 480 LYS B 181 CG CD CE NZ REMARK 480 LYS B 194 CD CE NZ 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 40 2.23 83.24 REMARK 500 ASP A 53 63.91 14.26 REMARK 500 ASP A 53 57.25 22.45 REMARK 500 ASN A 75 -120.71 59.51 REMARK 500 THR A 130 -75.11 -82.20 REMARK 500 TYR A 131 47.08 -91.88 REMARK 500 LYS A 144 41.28 74.12 REMARK 500 SER B 40 0.22 83.87 REMARK 500 GLU B 76 -9.92 69.04 REMARK 500 GLN B 89 28.57 -151.31 REMARK 500 LYS B 144 42.03 70.92 REMARK 500 ASN B 179 18.79 58.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 435 DISTANCE = 6.29 ANGSTROMS REMARK 525 HOH B 447 DISTANCE = 7.75 ANGSTROMS 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 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 44 OG1 REMARK 620 2 GDP A 301 O1B 73.0 REMARK 620 3 HOH A 404 O 80.1 72.4 REMARK 620 4 HOH A 406 O 80.3 92.9 158.3 REMARK 620 5 HOH A 407 O 164.8 91.8 94.9 101.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 44 OG1 REMARK 620 2 GDP B 301 O3B 92.9 REMARK 620 3 HOH B 401 O 89.1 79.6 REMARK 620 4 HOH B 405 O 173.1 83.5 96.0 REMARK 620 5 HOH B 413 O 89.4 92.5 172.0 84.9 REMARK 620 6 HOH B 428 O 90.3 176.5 101.9 93.1 86.0 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 GDP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BTB B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 303 DBREF 6Y7G A 1 227 UNP Q96E17 RAB3C_HUMAN 1 227 DBREF 6Y7G B 1 227 UNP Q96E17 RAB3C_HUMAN 1 227 SEQRES 1 A 227 MET ARG HIS GLU ALA PRO MET GLN MET ALA SER ALA GLN SEQRES 2 A 227 ASP ALA ARG TYR GLY GLN LYS ASP SER SER ASP GLN ASN SEQRES 3 A 227 PHE ASP TYR MET PHE LYS LEU LEU ILE ILE GLY ASN SER SEQRES 4 A 227 SER VAL GLY LYS THR SER PHE LEU PHE ARG TYR ALA ASP SEQRES 5 A 227 ASP SER PHE THR SER ALA PHE VAL SER THR VAL GLY ILE SEQRES 6 A 227 ASP PHE LYS VAL LYS THR VAL PHE LYS ASN GLU LYS ARG SEQRES 7 A 227 ILE LYS LEU GLN ILE TRP ASP THR ALA GLY GLN GLU ARG SEQRES 8 A 227 TYR ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET SEQRES 9 A 227 GLY PHE ILE LEU MET TYR ASP ILE THR ASN GLU GLU SER SEQRES 10 A 227 PHE ASN ALA VAL GLN ASP TRP SER THR GLN ILE LYS THR SEQRES 11 A 227 TYR SER TRP ASP ASN ALA GLN VAL ILE LEU VAL GLY ASN SEQRES 12 A 227 LYS CYS ASP MET GLU ASP GLU ARG VAL ILE SER THR GLU SEQRES 13 A 227 ARG GLY GLN HIS LEU GLY GLU GLN LEU GLY PHE GLU PHE SEQRES 14 A 227 PHE GLU THR SER ALA LYS ASP ASN ILE ASN VAL LYS GLN SEQRES 15 A 227 THR PHE GLU ARG LEU VAL ASP ILE ILE CYS ASP LYS MET SEQRES 16 A 227 SER GLU SER LEU GLU THR ASP PRO ALA ILE THR ALA ALA SEQRES 17 A 227 LYS GLN ASN THR ARG LEU LYS GLU THR PRO PRO PRO PRO SEQRES 18 A 227 GLN PRO ASN CYS ALA CYS SEQRES 1 B 227 MET ARG HIS GLU ALA PRO MET GLN MET ALA SER ALA GLN SEQRES 2 B 227 ASP ALA ARG TYR GLY GLN LYS ASP SER SER ASP GLN ASN SEQRES 3 B 227 PHE ASP TYR MET PHE LYS LEU LEU ILE ILE GLY ASN SER SEQRES 4 B 227 SER VAL GLY LYS THR SER PHE LEU PHE ARG TYR ALA ASP SEQRES 5 B 227 ASP SER PHE THR SER ALA PHE VAL SER THR VAL GLY ILE SEQRES 6 B 227 ASP PHE LYS VAL LYS THR VAL PHE LYS ASN GLU LYS ARG SEQRES 7 B 227 ILE LYS LEU GLN ILE TRP ASP THR ALA GLY GLN GLU ARG SEQRES 8 B 227 TYR ARG THR ILE THR THR ALA TYR TYR ARG GLY ALA MET SEQRES 9 B 227 GLY PHE ILE LEU MET TYR ASP ILE THR ASN GLU GLU SER SEQRES 10 B 227 PHE ASN ALA VAL GLN ASP TRP SER THR GLN ILE LYS THR SEQRES 11 B 227 TYR SER TRP ASP ASN ALA GLN VAL ILE LEU VAL GLY ASN SEQRES 12 B 227 LYS CYS ASP MET GLU ASP GLU ARG VAL ILE SER THR GLU SEQRES 13 B 227 ARG GLY GLN HIS LEU GLY GLU GLN LEU GLY PHE GLU PHE SEQRES 14 B 227 PHE GLU THR SER ALA LYS ASP ASN ILE ASN VAL LYS GLN SEQRES 15 B 227 THR PHE GLU ARG LEU VAL ASP ILE ILE CYS ASP LYS MET SEQRES 16 B 227 SER GLU SER LEU GLU THR ASP PRO ALA ILE THR ALA ALA SEQRES 17 B 227 LYS GLN ASN THR ARG LEU LYS GLU THR PRO PRO PRO PRO SEQRES 18 B 227 GLN PRO ASN CYS ALA CYS HET GDP A 301 28 HET BTB A 302 14 HET MG A 303 1 HET GDP B 301 28 HET BTB B 302 14 HET MG B 303 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETNAM MG MAGNESIUM ION HETSYN BTB BIS-TRIS BUFFER FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 BTB 2(C8 H19 N O5) FORMUL 5 MG 2(MG 2+) FORMUL 9 HOH *82(H2 O) HELIX 1 AA1 GLY A 42 ASP A 52 1 11 HELIX 2 AA2 ASN A 114 ALA A 120 1 7 HELIX 3 AA3 ALA A 120 TYR A 131 1 12 HELIX 4 AA4 MET A 147 ARG A 151 5 5 HELIX 5 AA5 SER A 154 GLY A 166 1 13 HELIX 6 AA6 ASN A 179 GLU A 197 1 19 HELIX 7 AA7 GLY B 42 ASP B 53 1 12 HELIX 8 AA8 GLU B 90 GLY B 102 1 13 HELIX 9 AA9 ASN B 114 ALA B 120 1 7 HELIX 10 AB1 ALA B 120 TYR B 131 1 12 HELIX 11 AB2 SER B 154 GLY B 166 1 13 HELIX 12 AB3 ASN B 179 SER B 196 1 18 SHEET 1 AA1 6 PHE A 67 LYS A 74 0 SHEET 2 AA1 6 LYS A 77 TRP A 84 -1 O ILE A 79 N VAL A 72 SHEET 3 AA1 6 TYR A 29 ILE A 36 1 N LEU A 33 O TRP A 84 SHEET 4 AA1 6 GLY A 105 ASP A 111 1 O MET A 109 N ILE A 36 SHEET 5 AA1 6 GLN A 137 ASN A 143 1 O ASN A 143 N TYR A 110 SHEET 6 AA1 6 GLU A 168 GLU A 171 1 O GLU A 168 N LEU A 140 SHEET 1 AA2 6 PHE B 67 LYS B 74 0 SHEET 2 AA2 6 LYS B 77 TRP B 84 -1 O ILE B 83 N LYS B 68 SHEET 3 AA2 6 TYR B 29 ILE B 36 1 N LEU B 33 O TRP B 84 SHEET 4 AA2 6 GLY B 105 ASP B 111 1 O MET B 109 N ILE B 36 SHEET 5 AA2 6 GLN B 137 ASN B 143 1 O ILE B 139 N LEU B 108 SHEET 6 AA2 6 GLU B 168 GLU B 171 1 O GLU B 168 N LEU B 140 LINK OG1 THR A 44 MG MG A 303 1555 1555 2.17 LINK O1B GDP A 301 MG MG A 303 1555 1555 2.34 LINK MG MG A 303 O HOH A 404 1555 1555 2.12 LINK MG MG A 303 O HOH A 406 1555 1555 2.13 LINK MG MG A 303 O HOH A 407 1555 1555 2.03 LINK OG1 THR B 44 MG MG B 303 1555 1555 1.94 LINK O3B GDP B 301 MG MG B 303 1555 1555 1.98 LINK MG MG B 303 O HOH B 401 1555 1555 2.27 LINK MG MG B 303 O HOH B 405 1555 1555 2.19 LINK MG MG B 303 O HOH B 413 1555 1555 2.19 LINK MG MG B 303 O HOH B 428 1555 1455 2.26 SITE 1 AC1 18 SER A 40 VAL A 41 GLY A 42 LYS A 43 SITE 2 AC1 18 THR A 44 SER A 45 PHE A 55 ASN A 143 SITE 3 AC1 18 LYS A 144 ASP A 146 MET A 147 SER A 173 SITE 4 AC1 18 ALA A 174 LYS A 175 MG A 303 HOH A 404 SITE 5 AC1 18 HOH A 407 HOH A 418 SITE 1 AC2 7 ASP A 146 MET A 147 GLU A 148 ASP A 149 SITE 2 AC2 7 GLU A 150 HIS B 160 GLN B 164 SITE 1 AC3 5 THR A 44 GDP A 301 HOH A 404 HOH A 406 SITE 2 AC3 5 HOH A 407 SITE 1 AC4 18 SER B 40 VAL B 41 GLY B 42 LYS B 43 SITE 2 AC4 18 THR B 44 SER B 45 PHE B 55 ASN B 143 SITE 3 AC4 18 LYS B 144 ASP B 146 MET B 147 SER B 173 SITE 4 AC4 18 ALA B 174 LYS B 175 MG B 303 HOH B 401 SITE 5 AC4 18 HOH B 405 HOH B 413 SITE 1 AC5 7 HIS A 160 GLN A 164 ASP B 146 MET B 147 SITE 2 AC5 7 GLU B 148 ASP B 149 GLU B 150 SITE 1 AC6 6 THR B 44 GDP B 301 HOH B 401 HOH B 405 SITE 2 AC6 6 HOH B 413 HOH B 428 CRYST1 40.190 40.434 66.362 86.02 74.16 66.45 P 1 2 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 0.024882 -0.010843 -0.007554 0.00000 SCALE2 0.000000 0.026978 0.001214 0.00000 SCALE3 0.000000 0.000000 0.015679 0.00000