PDB Short entry for 2IL1 HEADER PROTEIN TRANSPORT 02-OCT-06 2IL1 TITLE CRYSTAL STRUCTURE OF A PREDICTED HUMAN GTPASE IN COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB12; COMPND 3 CHAIN: A; 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: RAB12; 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-LIC KEYWDS G-PROTEIN, RAB, GDP, GTPASE, PREDICTED, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.WANG,Y.SHEN,W.TEMPEL,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 5 30-AUG-23 2IL1 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2IL1 1 REMARK REVDAT 3 13-JUL-11 2IL1 1 VERSN REVDAT 2 24-FEB-09 2IL1 1 VERSN REVDAT 1 10-OCT-06 2IL1 0 JRNL AUTH J.WANG,Y.SHEN,W.TEMPEL,R.LANDRY,C.H.ARROWSMITH,A.M.EDWARDS, JRNL AUTH 2 M.SUNDSTROM,J.WEIGELT,A.BOCHKAREV,H.PARK JRNL TITL CRYSTAL STRUCTURE OF A PREDICTED HUMAN GTPASE IN COMPLEX JRNL TITL 2 WITH GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 12316 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) : 0.241 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.994 REMARK 3 FREE R VALUE TEST SET COUNT : 615 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 800 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.25 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1278 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 24 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) : 39.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05600 REMARK 3 B22 (A**2) : -0.05600 REMARK 3 B33 (A**2) : 0.08500 REMARK 3 B12 (A**2) : -0.02800 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): 0.240 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1344 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1817 ; 1.415 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 167 ; 5.825 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 56 ;37.483 ;24.821 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 252 ;13.407 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;15.609 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 209 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 966 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 562 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 945 ; 0.294 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 54 ; 0.143 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.221 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.241 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.154 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.092 ; 0.200 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): 853 ; 2.439 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1324 ; 3.245 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 584 ; 2.740 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 491 ; 3.600 ; 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 134 A 304 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8095 23.2461 11.3459 REMARK 3 T TENSOR REMARK 3 T11: -0.2301 T22: -0.0191 REMARK 3 T33: -0.0760 T12: -0.0138 REMARK 3 T13: -0.0221 T23: -0.1146 REMARK 3 L TENSOR REMARK 3 L11: 1.6386 L22: 1.9427 REMARK 3 L33: 4.9988 L12: -0.2771 REMARK 3 L13: -0.4221 L23: 0.5848 REMARK 3 S TENSOR REMARK 3 S11: -0.0241 S12: 0.3424 S13: 0.0314 REMARK 3 S21: 0.0954 S22: -0.1986 S23: -0.0880 REMARK 3 S31: -0.1169 S32: -0.2105 S33: 0.2227 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 401 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5146 16.3399 13.9992 REMARK 3 T TENSOR REMARK 3 T11: -0.1618 T22: 0.2999 REMARK 3 T33: 0.0993 T12: -0.2522 REMARK 3 T13: 0.0727 T23: -0.3249 REMARK 3 L TENSOR REMARK 3 L11: 4.9557 L22: 14.2746 REMARK 3 L33: 19.2001 L12: -6.2115 REMARK 3 L13: 6.2350 L23: 0.7689 REMARK 3 S TENSOR REMARK 3 S11: 0.7446 S12: 0.1702 S13: -0.2873 REMARK 3 S21: 1.0879 S22: -0.2816 S23: 0.8937 REMARK 3 S31: 0.4352 S32: -0.7670 S33: -0.4630 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 2IL1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97625 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13543 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 13.90 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 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 1G17, CHAIN A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG4000, 0.2M CALCIUM ACETATE, REMARK 280 0.1M SODIUM CACODYLATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 210.30267 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 105.15133 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 157.72700 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 52.57567 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 262.87833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 210.30267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 105.15133 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 52.57567 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 157.72700 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 262.87833 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT OF THE REMARK 300 PROTEIN IS NOT 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 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 0.500000 -0.866025 0.000000 22.73150 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 39.37211 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 52.57567 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 CA CA A 501 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1004 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 113 REMARK 465 GLY A 114 REMARK 465 SER A 115 REMARK 465 SER A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 465 SER A 123 REMARK 465 SER A 124 REMARK 465 GLY A 125 REMARK 465 LEU A 126 REMARK 465 VAL A 127 REMARK 465 PRO A 128 REMARK 465 ARG A 129 REMARK 465 GLY A 130 REMARK 465 SER A 131 REMARK 465 PRO A 132 REMARK 465 ARG A 133 REMARK 465 ASP A 161 REMARK 465 THR A 162 REMARK 465 PHE A 163 REMARK 465 CYS A 164 REMARK 465 GLU A 165 REMARK 465 ALA A 166 REMARK 465 CYS A 167 REMARK 465 LYS A 168 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 LYS A 138 NZ REMARK 470 GLU A 181 CD OE1 OE2 REMARK 470 ARG A 183 NE CZ NH1 NH2 REMARK 470 LYS A 185 CD CE NZ REMARK 470 LYS A 186 CE NZ REMARK 470 ARG A 209 NE CZ NH1 NH2 REMARK 470 LYS A 223 CE NZ REMARK 470 GLU A 242 CG CD OE1 OE2 REMARK 470 GLN A 264 CD OE1 NE2 REMARK 470 LYS A 268 CD CE NZ REMARK 470 GLN A 271 OE1 NE2 REMARK 470 LYS A 284 CE NZ REMARK 470 LYS A 303 CD CE NZ 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 A 255 UNK UNX A 1404 2.15 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 CYS A 279 CB CYS A 279 SG -0.104 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 THR A 159 -109.24 -103.96 REMARK 500 LYS A 252 34.68 75.23 REMARK 500 CYS A 255 35.65 -95.70 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 152 OG1 REMARK 620 2 GDP A 401 O3B 83.8 REMARK 620 3 HOH A1013 O 80.6 89.6 REMARK 620 4 HOH A1014 O 84.6 69.0 155.1 REMARK 620 5 HOH A1015 O 84.9 165.2 97.9 100.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 290 OD2 REMARK 620 2 ASP A 290 OD2 84.1 REMARK 620 3 GLU A 291 OE1 100.4 164.9 REMARK 620 4 GLU A 291 OE2 101.5 142.7 51.0 REMARK 620 5 GLU A 291 OE1 171.4 94.2 83.5 74.9 REMARK 620 6 GLU A 291 OE2 140.2 93.6 73.7 103.9 48.2 REMARK 620 7 HOH A1001 O 73.3 78.7 88.6 138.4 114.6 67.3 REMARK 620 8 HOH A1001 O 83.1 73.0 121.7 71.2 88.4 134.2 144.8 REMARK 620 N 1 2 3 4 5 6 7 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 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNX A 1406 DBREF 2IL1 A 132 304 UNP Q86YS6 RAB43_HUMAN 16 165 SEQADV 2IL1 MET A 113 UNP Q86YS6 INITIATING METHIONINE SEQADV 2IL1 GLY A 114 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 SER A 115 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 SER A 116 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 HIS A 117 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 HIS A 118 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 HIS A 119 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 HIS A 120 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 HIS A 121 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 HIS A 122 UNP Q86YS6 EXPRESSION TAG SEQADV 2IL1 SER A 123 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 SER A 124 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 GLY A 125 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 LEU A 126 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 VAL A 127 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 PRO A 128 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 ARG A 129 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 GLY A 130 UNP Q86YS6 CLONING ARTIFACT SEQADV 2IL1 SER A 131 UNP Q86YS6 CLONING ARTIFACT SEQRES 1 A 192 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 192 LEU VAL PRO ARG GLY SER PRO ARG PRO ALA ASP PHE LYS SEQRES 3 A 192 LEU GLN VAL ILE ILE ILE GLY SER ARG GLY VAL GLY LYS SEQRES 4 A 192 THR SER LEU MET GLU ARG PHE THR ASP ASP THR PHE CYS SEQRES 5 A 192 GLU ALA CYS LYS SER THR VAL GLY VAL ASP PHE LYS ILE SEQRES 6 A 192 LYS THR VAL GLU LEU ARG GLY LYS LYS ILE ARG LEU GLN SEQRES 7 A 192 ILE TRP ASP THR ALA GLY GLN GLU ARG PHE ASN SER ILE SEQRES 8 A 192 THR SER ALA TYR TYR ARG SER ALA LYS GLY ILE ILE LEU SEQRES 9 A 192 VAL TYR ASP ILE THR LYS LYS GLU THR PHE ASP ASP LEU SEQRES 10 A 192 PRO LYS TRP MET LYS MET ILE ASP LYS TYR ALA SER GLU SEQRES 11 A 192 ASP ALA GLU LEU LEU LEU VAL GLY ASN LYS LEU ASP CYS SEQRES 12 A 192 GLU THR ASP ARG GLU ILE THR ARG GLN GLN GLY GLU LYS SEQRES 13 A 192 PHE ALA GLN GLN ILE THR GLY MET ARG PHE CYS GLU ALA SEQRES 14 A 192 SER ALA LYS ASP ASN PHE ASN VAL ASP GLU ILE PHE LEU SEQRES 15 A 192 LYS LEU VAL ASP ASP ILE LEU LYS LYS MET HET MG A 402 1 HET CA A 501 1 HET GDP A 401 28 HET UNX A1401 1 HET UNX A1402 1 HET UNX A1403 1 HET UNX A1404 1 HET UNX A1405 1 HET UNX A1406 1 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 2 MG MG 2+ FORMUL 3 CA CA 2+ FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 UNX 6(X) FORMUL 11 HOH *24(H2 O) HELIX 1 1 GLY A 150 THR A 159 1 10 HELIX 2 2 GLN A 197 ARG A 199 5 3 HELIX 3 3 PHE A 200 ALA A 211 1 12 HELIX 4 4 LYS A 222 ASP A 228 1 7 HELIX 5 5 ASP A 228 ALA A 240 1 13 HELIX 6 6 LYS A 252 ARG A 259 5 8 HELIX 7 7 THR A 262 GLN A 272 1 11 HELIX 8 8 ASN A 288 LYS A 303 1 16 SHEET 1 A 6 VAL A 173 LEU A 182 0 SHEET 2 A 6 LYS A 185 THR A 194 -1 O LEU A 189 N LYS A 178 SHEET 3 A 6 PHE A 137 ILE A 144 1 N PHE A 137 O ARG A 188 SHEET 4 A 6 GLY A 213 ASP A 219 1 O ILE A 215 N ILE A 144 SHEET 5 A 6 GLU A 245 ASN A 251 1 O ASN A 251 N TYR A 218 SHEET 6 A 6 ARG A 277 GLU A 280 1 O ARG A 277 N LEU A 248 LINK OG1 THR A 152 MG MG A 402 1555 1555 2.35 LINK OD2 ASP A 290 CA CA A 501 1555 1555 2.20 LINK OD2 ASP A 290 CA CA A 501 10665 1555 2.33 LINK OE1 GLU A 291 CA CA A 501 1555 1555 2.48 LINK OE2 GLU A 291 CA CA A 501 1555 1555 2.56 LINK OE1 GLU A 291 CA CA A 501 10665 1555 2.58 LINK OE2 GLU A 291 CA CA A 501 10665 1555 2.72 LINK O3B GDP A 401 MG MG A 402 1555 1555 2.43 LINK MG MG A 402 O HOH A1013 1555 1555 2.02 LINK MG MG A 402 O HOH A1014 1555 1555 2.50 LINK MG MG A 402 O HOH A1015 1555 1555 2.42 LINK CA CA A 501 O HOH A1001 1555 1555 2.59 LINK CA CA A 501 O HOH A1001 1555 10665 2.50 SITE 1 AC1 5 THR A 152 GDP A 401 HOH A1013 HOH A1014 SITE 2 AC1 5 HOH A1015 SITE 1 AC2 3 ASP A 290 GLU A 291 HOH A1001 SITE 1 AC3 17 ARG A 147 GLY A 148 VAL A 149 GLY A 150 SITE 2 AC3 17 LYS A 151 THR A 152 SER A 153 ASN A 251 SITE 3 AC3 17 LYS A 252 ASP A 254 CYS A 255 SER A 282 SITE 4 AC3 17 ALA A 283 LYS A 284 MG A 402 HOH A1014 SITE 5 AC3 17 UNX A1404 SITE 1 AC4 2 CYS A 279 ASN A 288 SITE 1 AC5 5 ARG A 199 PHE A 200 SER A 202 ILE A 203 SITE 2 AC5 5 GLN A 272 SITE 1 AC6 2 ASP A 254 ASP A 285 SITE 1 AC7 2 CYS A 255 GDP A 401 SITE 1 AC8 3 ALA A 195 LYS A 234 ASP A 237 SITE 1 AC9 3 ASP A 254 GLU A 256 THR A 257 CRYST1 45.463 45.463 315.454 90.00 90.00 120.00 P 65 2 2 12 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 0.021996 0.012699 0.000000 0.00000 SCALE2 0.000000 0.025399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003170 0.00000