HEADER HYDROLASE ACTIVATOR/PROTEIN TRANSPORT 26-MAR-13 4JVS TITLE CRYSTAL STRUCTURE OF LEPB GAP DOMAIN FROM LEGIONELLA DRANCOURTII IN TITLE 2 COMPLEX WITH RAB1-GDP AND ALF3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GAP DOMAIN, UNP RESIDUES 316-620; COMPND 5 SYNONYM: GTPASE ACTIVATING PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RAS-RELATED PROTEIN RAB-1A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 1-177; COMPND 11 SYNONYM: RAS SUPERFAMILY OF MONOMERIC G PROTEIN, YPT1-RELATED COMPND 12 PROTEIN; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA DRANCOURTII; SOURCE 3 ORGANISM_TAXID: 658187; SOURCE 4 STRAIN: LLAP12; SOURCE 5 GENE: LDG_7216; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RAB1A; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS NEW GAP FOLD, BIND AND HYDROLYZE GUANOSINE TRIPHOSPHATE, RAB1 KEYWDS 2 BINDING, HYDROLASE ACTIVATOR-PROTEIN TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.YU,Q.YAO,D.-C.WANG,F.SHAO REVDAT 3 20-MAR-24 4JVS 1 REMARK SEQADV LINK REVDAT 2 14-AUG-13 4JVS 1 JRNL REVDAT 1 08-MAY-13 4JVS 0 JRNL AUTH Q.YU,L.HU,Q.YAO,Y.ZHU,N.DONG,D.-C.WANG,F.SHAO JRNL TITL STRUCTURAL ANALYSES OF LEGIONELLA LEPB REVEAL A NEW GAP FOLD JRNL TITL 2 THAT CATALYTICALLY MIMICS EUKARYOTIC RASGAP JRNL REF CELL RES. V. 23 775 2013 JRNL REFN ISSN 1001-0602 JRNL PMID 23588383 JRNL DOI 10.1038/CR.2013.54 REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8_1069 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 13976 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.9610 - 4.7422 1.00 2854 131 0.2094 0.2365 REMARK 3 2 4.7422 - 3.7724 1.00 2659 146 0.1876 0.2210 REMARK 3 3 3.7724 - 3.2979 1.00 2615 148 0.2277 0.2723 REMARK 3 4 3.2979 - 2.9975 1.00 2608 128 0.2672 0.2971 REMARK 3 5 2.9975 - 2.7833 0.98 2538 149 0.2924 0.3792 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.960 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 40.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 3722 REMARK 3 ANGLE : 1.503 5040 REMARK 3 CHIRALITY : 0.097 556 REMARK 3 PLANARITY : 0.011 648 REMARK 3 DIHEDRAL : 19.373 1374 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078566. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14058 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM ACETATE, 0.1M TRIS, REMARK 280 25%(W/V) POLYETHYLENE GLYCOL 3350, PH 8.5, EVAPORATION, REMARK 280 TEMPERATURE 298.0K 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 131.81600 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 65.90800 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 98.86200 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 32.95400 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 164.77000 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 131.81600 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 65.90800 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 32.95400 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 98.86200 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 164.77000 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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 SER A 311 REMARK 465 GLY A 312 REMARK 465 ARG A 313 REMARK 465 PRO A 314 REMARK 465 MET A 315 REMARK 465 THR A 316 REMARK 465 LEU A 317 REMARK 465 GLN A 318 REMARK 465 SER A 319 REMARK 465 ALA A 320 REMARK 465 MET A 321 REMARK 465 GLY A 322 REMARK 465 ASP A 323 REMARK 465 MET A 324 REMARK 465 TYR A 325 REMARK 465 GLN A 326 REMARK 465 SER A 327 REMARK 465 ILE A 328 REMARK 465 PHE A 329 REMARK 465 VAL A 330 REMARK 465 PHE A 497 REMARK 465 MET A 498 REMARK 465 LYS A 499 REMARK 465 GLU A 500 REMARK 465 LYS A 501 REMARK 465 SER A 531 REMARK 465 GLU A 532 REMARK 465 VAL A 533 REMARK 465 MET A 622 REMARK 465 THR A 623 REMARK 465 THR A 624 REMARK 465 SER B -3 REMARK 465 GLY B -2 REMARK 465 ARG B -1 REMARK 465 PRO B 0 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 MET B 4 REMARK 465 ASN B 5 REMARK 465 PRO B 6 REMARK 465 GLY B 177 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 ASP A 526 CG OD1 OD2 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 CE1 HIS A 539 O SER A 541 1.43 REMARK 500 O ILE A 547 NH1 ARG A 579 1.59 REMARK 500 NH2 ARG A 579 O ACY A 701 1.60 REMARK 500 O1B GDP B 400 AL AF3 B 401 1.64 REMARK 500 O1B GDP B 400 F2 AF3 B 401 1.87 REMARK 500 OE2 GLU A 346 NH1 ARG A 349 1.92 REMARK 500 OE2 GLU B 38 O2' GDP B 400 1.92 REMARK 500 NE2 HIS A 539 O PHE A 544 2.07 REMARK 500 OG SER B 42 F3 AF3 B 401 2.07 REMARK 500 NE2 HIS A 539 O SER A 541 2.19 REMARK 500 NZ LYS A 427 ND1 HIS A 539 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SG CYS A 607 SG CYS A 607 10555 1.35 REMARK 500 NH2 ARG A 398 OD2 ASP A 592 6554 2.19 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 PRO A 410 C - N - CD ANGL. DEV. = -29.1 DEGREES REMARK 500 LEU A 493 CA - CB - CG ANGL. DEV. = 13.9 DEGREES REMARK 500 PRO A 503 C - N - CD ANGL. DEV. = -18.8 DEGREES REMARK 500 ASP A 540 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 GLN B 70 OE1 - CD - NE2 ANGL. DEV. = -17.3 DEGREES REMARK 500 GLN B 70 CG - CD - NE2 ANGL. DEV. = 17.3 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 GLU A 341 21.05 -153.16 REMARK 500 SER A 436 -4.07 -141.10 REMARK 500 GLN A 491 75.61 -69.09 REMARK 500 LEU A 493 -108.72 -51.12 REMARK 500 GLU A 494 119.91 -161.87 REMARK 500 ASP A 495 99.55 58.55 REMARK 500 ASP A 584 -63.26 67.67 REMARK 500 ASP B 34 18.17 59.11 REMARK 500 ASP B 56 42.06 38.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 409 PRO A 410 140.86 REMARK 500 ASN A 489 GLY A 490 114.69 REMARK 500 ASP A 540 SER A 541 139.59 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 B 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 25 OG REMARK 620 2 THR B 43 OG1 63.9 REMARK 620 3 GDP B 400 O2B 53.7 101.6 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AF3 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JW1 RELATED DB: PDB DBREF 4JVS A 316 624 UNP G9EPL4 G9EPL4_9GAMM 316 620 DBREF 4JVS B 1 177 UNP P62820 RAB1A_HUMAN 1 177 SEQADV 4JVS SER A 311 UNP G9EPL4 EXPRESSION TAG SEQADV 4JVS GLY A 312 UNP G9EPL4 EXPRESSION TAG SEQADV 4JVS ARG A 313 UNP G9EPL4 EXPRESSION TAG SEQADV 4JVS PRO A 314 UNP G9EPL4 EXPRESSION TAG SEQADV 4JVS MET A 315 UNP G9EPL4 EXPRESSION TAG SEQADV 4JVS SER B -3 UNP P62820 EXPRESSION TAG SEQADV 4JVS GLY B -2 UNP P62820 EXPRESSION TAG SEQADV 4JVS ARG B -1 UNP P62820 EXPRESSION TAG SEQADV 4JVS PRO B 0 UNP P62820 EXPRESSION TAG SEQRES 1 A 310 SER GLY ARG PRO MET THR LEU GLN SER ALA MET GLY ASP SEQRES 2 A 310 MET TYR GLN SER ILE PHE VAL ALA THR PRO PRO LEU LEU SEQRES 3 A 310 GLN MET GLU GLN GLU GLN PRO PHE PRO GLU LEU ILE ARG SEQRES 4 A 310 THR TRP ALA GLY LEU LEU GLY GLN ILE GLY VAL GLU SER SEQRES 5 A 310 VAL ARG THR GLU GLU VAL ASN PHE GLY GLN LEU ALA LYS SEQRES 6 A 310 CYS PHE ASN ASP TYR LEU ASN THR VAL ALA GLU HIS CYS SEQRES 7 A 310 GLU GLN GLN ASN ILE TRP GLN HIS LYS ARG GLU GLU ASN SEQRES 8 A 310 HIS ASN PHE PHE THR ALA PHE LYS PRO ASP ALA SER LYS SEQRES 9 A 310 ALA ALA LEU HIS GLY HIS ALA TYR ILE ALA HIS TYR LYS SEQRES 10 A 310 GLU SER VAL ILE LEU ARG HIS LEU SER ILE VAL ASP PRO SEQRES 11 A 310 LYS THR LEU GLY MET LEU ARG PHE ALA PRO TYR GLU ALA SEQRES 12 A 310 PRO SER THR ASP TYR CYS ARG HIS PHE PRO ASP SER PRO SEQRES 13 A 310 TRP ALA LYS MET GLN ARG LEU ALA THR ALA GLY GLN ASN SEQRES 14 A 310 ILE ILE LEU GLN LEU ARG LEU ILE GLN ASN GLY GLN MET SEQRES 15 A 310 LEU GLU ASP ASP PHE MET LYS GLU LYS LEU PRO VAL LEU SEQRES 16 A 310 GLN LYS ALA LEU ASP ASP PHE MET GLN TYR LYS THR GLU SEQRES 17 A 310 VAL ASP ALA LEU LEU ALA HIS ASP SER GLU VAL THR PRO SEQRES 18 A 310 VAL SER THR HIS ASP SER SER PHE PHE TYR ASP ILE ASP SEQRES 19 A 310 GLU GLN THR LEU ASN ALA MET SER GLY ASP GLN LEU ALA SEQRES 20 A 310 THR ILE CYS PHE GLU GLU LEU ASN ALA PRO HIS PRO SER SEQRES 21 A 310 ARG LEU ILE MET ARG ILE LEU LYS SER ASP SER LEU TRP SEQRES 22 A 310 GLN GLU VAL ASP ASP SER LEU ASN GLY ASP ALA PHE MET SEQRES 23 A 310 GLY ARG GLN ASP ASP ILE CYS GLU LYS ARG ASN LYS ILE SEQRES 24 A 310 CYS GLN TRP ARG GLN LEU VAL GLN MET THR THR SEQRES 1 B 181 SER GLY ARG PRO MET SER SER MET ASN PRO GLU TYR ASP SEQRES 2 B 181 TYR LEU PHE LYS LEU LEU LEU ILE GLY ASP SER GLY VAL SEQRES 3 B 181 GLY LYS SER CYS LEU LEU LEU ARG PHE ALA ASP ASP THR SEQRES 4 B 181 TYR THR GLU SER TYR ILE SER THR ILE GLY VAL ASP PHE SEQRES 5 B 181 LYS ILE ARG THR ILE GLU LEU ASP GLY LYS THR ILE LYS SEQRES 6 B 181 LEU GLN ILE TRP ASP THR ALA GLY GLN GLU ARG PHE ARG SEQRES 7 B 181 THR ILE THR SER SER TYR TYR ARG GLY ALA HIS GLY ILE SEQRES 8 B 181 ILE VAL VAL TYR ASP VAL THR ASP GLN GLU SER PHE ASN SEQRES 9 B 181 ASN VAL LYS GLN TRP LEU GLN GLU ILE ASP ARG TYR ALA SEQRES 10 B 181 SER GLU ASN VAL ASN LYS LEU LEU VAL GLY ASN LYS CYS SEQRES 11 B 181 ASP LEU THR THR LYS LYS VAL VAL ASP TYR THR THR ALA SEQRES 12 B 181 LYS GLU PHE ALA ASP SER LEU GLY ILE PRO PHE LEU GLU SEQRES 13 B 181 THR SER ALA LYS ASN ALA THR ASN VAL GLU GLN SER PHE SEQRES 14 B 181 MET THR MET ALA ALA GLU ILE LYS LYS ARG MET GLY HET ACY A 701 4 HET GDP B 400 28 HET AF3 B 401 4 HET MG B 402 1 HETNAM ACY ACETIC ACID HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM AF3 ALUMINUM FLUORIDE HETNAM MG MAGNESIUM ION FORMUL 3 ACY C2 H4 O2 FORMUL 4 GDP C10 H15 N5 O11 P2 FORMUL 5 AF3 AL F3 FORMUL 6 MG MG 2+ FORMUL 7 HOH *4(H2 O) HELIX 1 1 PRO A 343 GLY A 356 1 14 HELIX 2 2 ASN A 369 GLN A 391 1 23 HELIX 3 3 PHE A 405 LYS A 409 5 5 HELIX 4 4 LYS A 427 LEU A 435 1 9 HELIX 5 5 PHE A 448 PRO A 450 5 3 HELIX 6 6 TYR A 451 PHE A 462 1 12 HELIX 7 7 SER A 465 GLN A 488 1 24 HELIX 8 8 PRO A 503 HIS A 525 1 23 HELIX 9 9 ASP A 548 ASN A 553 1 6 HELIX 10 10 SER A 556 LEU A 568 1 13 HELIX 11 11 SER A 574 LYS A 582 1 9 HELIX 12 12 ASP A 584 ASN A 595 1 12 HELIX 13 13 ASP A 605 GLN A 621 1 17 HELIX 14 14 GLY B 23 ASP B 34 1 12 HELIX 15 15 GLN B 70 ARG B 72 5 3 HELIX 16 16 PHE B 73 SER B 79 1 7 HELIX 17 17 ASP B 95 ASN B 101 1 7 HELIX 18 18 ASN B 101 ALA B 113 1 13 HELIX 19 19 ASP B 135 SER B 145 1 11 HELIX 20 20 ASN B 160 ARG B 175 1 16 SHEET 1 A 2 ALA A 416 LEU A 417 0 SHEET 2 A 2 HIS A 420 ALA A 421 -1 O HIS A 420 N LEU A 417 SHEET 1 B 2 MET A 445 LEU A 446 0 SHEET 2 B 2 ILE B 41 SER B 42 -1 O SER B 42 N MET A 445 SHEET 1 C 6 VAL B 46 LEU B 55 0 SHEET 2 C 6 LYS B 58 THR B 67 -1 O LYS B 58 N LEU B 55 SHEET 3 C 6 TYR B 10 GLY B 18 1 N LEU B 16 O TRP B 65 SHEET 4 C 6 GLY B 86 ASP B 92 1 O ILE B 88 N LEU B 15 SHEET 5 C 6 ASN B 118 ASN B 124 1 O ASN B 124 N TYR B 91 SHEET 6 C 6 PHE B 150 GLU B 152 1 O LEU B 151 N GLY B 123 LINK OG SER B 25 MG MG B 402 1555 1555 2.70 LINK OG1 THR B 43 MG MG B 402 1555 1555 1.98 LINK O2B GDP B 400 MG MG B 402 1555 1555 2.05 CISPEP 1 PRO A 410 ASP A 411 0 -2.83 CISPEP 2 GLU A 494 ASP A 495 0 19.17 CISPEP 3 ASP A 495 ASP A 496 0 -8.78 SITE 1 AC1 5 ASP A 540 SER A 541 ASP A 546 ILE A 547 SITE 2 AC1 5 ARG A 579 SITE 1 AC2 20 ARG A 447 GLY B 21 VAL B 22 GLY B 23 SITE 2 AC2 20 LYS B 24 SER B 25 CYS B 26 TYR B 36 SITE 3 AC2 20 GLU B 38 TYR B 40 THR B 43 ASN B 124 SITE 4 AC2 20 LYS B 125 ASP B 127 LEU B 128 SER B 154 SITE 5 AC2 20 ALA B 155 LYS B 156 AF3 B 401 MG B 402 SITE 1 AC3 11 ARG A 447 SER B 20 GLY B 21 LYS B 24 SITE 2 AC3 11 SER B 42 THR B 43 GLY B 69 GLN B 70 SITE 3 AC3 11 GDP B 400 MG B 402 HOH B 502 SITE 1 AC4 5 SER B 25 THR B 43 THR B 67 GDP B 400 SITE 2 AC4 5 AF3 B 401 CRYST1 95.561 95.561 197.724 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 0.010465 0.006042 0.000000 0.00000 SCALE2 0.000000 0.012083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005058 0.00000