PDB Short entry for 3JZA HEADER TRANSPORT PROTEIN 23-SEP-09 3JZA TITLE CRYSTAL STRUCTURE OF HUMAN RAB1B IN COMPLEX WITH THE GEF DOMAIN OF TITLE 2 DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 3-174; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UNCHARACTERIZED PROTEIN DRRA; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: GEF DOMAIN: UNP RESIDUES 340-533; COMPND 10 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: RAB1B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET19MOD_TEV; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. SOURCE 13 PHILADELPHIA 1; SOURCE 14 ORGANISM_TAXID: 272624; SOURCE 15 STRAIN: PHILADELPHIA 1 / DSM 7513; SOURCE 16 ATCC: 33152; SOURCE 17 GENE: LPG2464; SOURCE 18 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 19 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 20 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 21 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 22 EXPRESSION_SYSTEM_PLASMID: PET19MOD_TEV KEYWDS RABGDI, RABGEF, GDI, GEF, GDF, GDI DISPLACEMENT FACTOR, GTP-BINDING, KEYWDS 2 LIPOPROTEIN, MEMBRANE, NUCLEOTIDE-BINDING, PRENYLATION, PROTEIN KEYWDS 3 TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHOEBEL,L.K.OESTERLIN,W.BLANKENFELDT,R.S.GOODY,A.ITZEN REVDAT 3 01-NOV-17 3JZA 1 REMARK REVDAT 2 13-JUL-11 3JZA 1 VERSN REVDAT 1 19-JAN-10 3JZA 0 JRNL AUTH S.SCHOEBEL,L.K.OESTERLIN,W.BLANKENFELDT,R.S.GOODY,A.ITZEN JRNL TITL RABGDI DISPLACEMENT BY DRRA FROM LEGIONELLA IS A CONSEQUENCE JRNL TITL 2 OF ITS GUANINE NUCLEOTIDE EXCHANGE ACTIVITY. JRNL REF MOL.CELL V. 36 1060 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 20064470 JRNL DOI 10.1016/J.MOLCEL.2009.11.014 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.P.MACHNER,R.R.ISBERG REMARK 1 TITL A BIFUNCTIONAL BACTERIAL PROTEIN LINKS GDI DISPLACEMENT TO REMARK 1 TITL 2 RAB1 ACTIVATION. REMARK 1 REF SCIENCE V. 318 974 2007 REMARK 1 REFN ISSN 0036-8075 REMARK 1 PMID 17947549 REMARK 1 DOI 10.1126/SCIENCE.1149121 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.INGMUNDSON,A.DELPRATO,D.G.LAMBRIGHT,C.R.ROY REMARK 1 TITL LEGIONELLA PNEUMOPHILA PROTEINS THAT REGULATE RAB1 MEMBRANE REMARK 1 TITL 2 CYCLING. REMARK 1 REF NATURE V. 450 365 2007 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 17952054 REMARK 1 DOI 10.1038/NATURE06336 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0070 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.63 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 40517 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2732 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2818 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 246 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 33.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.79000 REMARK 3 B22 (A**2) : -2.79000 REMARK 3 B33 (A**2) : 4.19000 REMARK 3 B12 (A**2) : -1.40000 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): 0.127 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.094 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.800 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2906 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1955 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3935 ; 1.829 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4816 ; 1.050 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 374 ; 6.405 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 126 ;34.354 ;25.397 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 540 ;14.364 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.583 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3212 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 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): 1816 ; 1.292 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 738 ; 0.464 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2928 ; 2.067 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1090 ; 3.123 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 999 ; 4.731 ; 4.500 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 : 3 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 : B 340 B 462 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0639 -7.5585 19.8279 REMARK 3 T TENSOR REMARK 3 T11: 0.0818 T22: 0.0934 REMARK 3 T33: 0.0561 T12: 0.0278 REMARK 3 T13: -0.0278 T23: -0.0677 REMARK 3 L TENSOR REMARK 3 L11: 0.8452 L22: 1.7970 REMARK 3 L33: 1.1294 L12: -0.6708 REMARK 3 L13: -0.5621 L23: 0.6717 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: -0.1008 S13: 0.0818 REMARK 3 S21: 0.1575 S22: 0.0163 S23: 0.0257 REMARK 3 S31: -0.0982 S32: 0.0075 S33: 0.0012 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 : B 463 B 532 REMARK 3 ORIGIN FOR THE GROUP (A): 28.9077 -13.7315 -0.5561 REMARK 3 T TENSOR REMARK 3 T11: 0.0799 T22: 0.1137 REMARK 3 T33: 0.1240 T12: -0.0315 REMARK 3 T13: -0.0548 T23: 0.0505 REMARK 3 L TENSOR REMARK 3 L11: 2.4332 L22: 2.0423 REMARK 3 L33: 1.5825 L12: 0.0322 REMARK 3 L13: 0.7428 L23: 0.3900 REMARK 3 S TENSOR REMARK 3 S11: -0.1739 S12: 0.2617 S13: 0.4915 REMARK 3 S21: -0.2038 S22: 0.0109 S23: -0.0951 REMARK 3 S31: -0.1587 S32: 0.2162 S33: 0.1630 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 151 REMARK 3 RESIDUE RANGE : A 157 A 173 REMARK 3 ORIGIN FOR THE GROUP (A): 24.8045 -30.7124 20.9262 REMARK 3 T TENSOR REMARK 3 T11: 0.1820 T22: 0.1970 REMARK 3 T33: 0.0826 T12: 0.0416 REMARK 3 T13: 0.0229 T23: -0.0319 REMARK 3 L TENSOR REMARK 3 L11: 3.6059 L22: 1.0431 REMARK 3 L33: 0.8958 L12: 0.0840 REMARK 3 L13: -0.5123 L23: 0.0017 REMARK 3 S TENSOR REMARK 3 S11: -0.1908 S12: -0.4787 S13: -0.2710 REMARK 3 S21: 0.1427 S22: 0.0026 S23: 0.0342 REMARK 3 S31: 0.2062 S32: 0.0410 S33: 0.1882 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY. REMARK 4 REMARK 4 3JZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000000 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40529 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP, DM 6.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 35% V/V PEG 600, REMARK 280 PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 0.00000 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 0.00000 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 73.18000 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 73.18000 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 73.18000 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 0.00000 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 0.00000 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 73.18000 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 73.18000 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 73.18000 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYMMETRIC UNIT. 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: 3370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.8 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 GLY A 0 REMARK 465 HIS A 1 REMARK 465 MET A 2 REMARK 465 PRO A 3 REMARK 465 ALA A 152 REMARK 465 LYS A 153 REMARK 465 GLY A 174 REMARK 465 GLY B 337 REMARK 465 HIS B 338 REMARK 465 MET B 339 REMARK 465 LYS B 533 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 LEU A 125 CG CD1 CD2 REMARK 470 THR A 126 OG1 CG2 REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLN A 160 CG CD OE1 NE2 REMARK 470 GLU B 528 CG CD OE1 OE2 REMARK 470 TYR B 532 CG CD1 CD2 CE1 CE2 CZ OH 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 CD2 LEU B 375 O HOH B 204 1.76 REMARK 500 OE1 GLU B 347 O HOH B 187 1.91 REMARK 500 ND2 ASN B 437 O HOH B 236 1.92 REMARK 500 O HOH A 198 O HOH B 235 1.93 REMARK 500 CG ASN B 437 O HOH B 236 2.00 REMARK 500 OD1 ASN B 348 O HOH B 142 2.02 REMARK 500 O ASP A 107 O HOH A 207 2.08 REMARK 500 O HOH A 266 O HOH A 268 2.11 REMARK 500 OG SER B 366 O HOH B 101 2.18 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 O HOH A 265 O HOH B 196 9555 2.18 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 VAL A 87 CB VAL A 87 CG1 0.158 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 ASP A 89 CB - CG - OD1 ANGL. DEV. = 5.5 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 VAL A 130 -12.74 -143.05 REMARK 500 SER B 426 21.35 -142.49 REMARK 500 TRP B 486 -123.66 51.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 365 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JZ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE GEF DOMAIN OF DRRA/SIDM FROM LEGIONELLA REMARK 900 PNEUMOPHILA DBREF 3JZA A 3 174 UNP Q9H0U4 RAB1B_HUMAN 3 174 DBREF 3JZA B 340 533 UNP Q5ZSQ3 Q5ZSQ3_LEGPH 340 533 SEQADV 3JZA GLY A 0 UNP Q9H0U4 EXPRESSION TAG SEQADV 3JZA HIS A 1 UNP Q9H0U4 EXPRESSION TAG SEQADV 3JZA MET A 2 UNP Q9H0U4 EXPRESSION TAG SEQADV 3JZA GLY B 337 UNP Q5ZSQ3 EXPRESSION TAG SEQADV 3JZA HIS B 338 UNP Q5ZSQ3 EXPRESSION TAG SEQADV 3JZA MET B 339 UNP Q5ZSQ3 EXPRESSION TAG SEQRES 1 A 175 GLY HIS MET PRO GLU TYR ASP TYR LEU PHE LYS LEU LEU SEQRES 2 A 175 LEU ILE GLY ASP SER GLY VAL GLY LYS SER CYS LEU LEU SEQRES 3 A 175 LEU ARG PHE ALA ASP ASP THR TYR THR GLU SER TYR ILE SEQRES 4 A 175 SER THR ILE GLY VAL ASP PHE LYS ILE ARG THR ILE GLU SEQRES 5 A 175 LEU ASP GLY LYS THR ILE LYS LEU GLN ILE TRP ASP THR SEQRES 6 A 175 ALA GLY GLN GLU ARG PHE ARG THR ILE THR SER SER TYR SEQRES 7 A 175 TYR ARG GLY ALA HIS GLY ILE ILE VAL VAL TYR ASP VAL SEQRES 8 A 175 THR ASP GLN GLU SER TYR ALA ASN VAL LYS GLN TRP LEU SEQRES 9 A 175 GLN GLU ILE ASP ARG TYR ALA SER GLU ASN VAL ASN LYS SEQRES 10 A 175 LEU LEU VAL GLY ASN LYS SER ASP LEU THR THR LYS LYS SEQRES 11 A 175 VAL VAL ASP ASN THR THR ALA LYS GLU PHE ALA ASP SER SEQRES 12 A 175 LEU GLY ILE PRO PHE LEU GLU THR SER ALA LYS ASN ALA SEQRES 13 A 175 THR ASN VAL GLU GLN ALA PHE MET THR MET ALA ALA GLU SEQRES 14 A 175 ILE LYS LYS ARG MET GLY SEQRES 1 B 197 GLY HIS MET VAL THR ARG ILE GLU ASN LEU GLU ASN ALA SEQRES 2 B 197 LYS LYS LEU TRP ASP ASN ALA ASN SER MET LEU GLU LYS SEQRES 3 B 197 GLY ASN ILE SER GLY TYR LEU LYS ALA ALA ASN GLU LEU SEQRES 4 B 197 HIS LYS PHE MET LYS GLU LYS ASN LEU LYS GLU ASP ASP SEQRES 5 B 197 LEU ARG PRO GLU LEU SER ASP LYS THR ILE SER PRO LYS SEQRES 6 B 197 GLY TYR ALA ILE LEU GLN SER LEU TRP GLY ALA ALA SER SEQRES 7 B 197 ASP TYR SER ARG ALA ALA ALA THR LEU THR GLU SER THR SEQRES 8 B 197 VAL GLU PRO GLY LEU VAL SER ALA VAL ASN LYS MET SER SEQRES 9 B 197 ALA PHE PHE MET ASP CYS LYS LEU SER PRO ASN GLU ARG SEQRES 10 B 197 ALA THR PRO ASP PRO ASP PHE LYS VAL GLY LYS SER LYS SEQRES 11 B 197 ILE LEU VAL GLY ILE MET GLN PHE ILE LYS ASP VAL ALA SEQRES 12 B 197 ASP PRO THR SER LYS ILE TRP MET HIS ASN THR LYS ALA SEQRES 13 B 197 LEU MET ASN HIS LYS ILE ALA ALA ILE GLN LYS LEU GLU SEQRES 14 B 197 ARG SER ASN ASN VAL ASN ASP GLU THR LEU GLU SER VAL SEQRES 15 B 197 LEU SER SER LYS GLY GLU ASN LEU SER GLU TYR LEU SER SEQRES 16 B 197 TYR LYS HET PO4 A 365 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *246(H2 O) HELIX 1 1 GLY A 20 LEU A 25 5 6 HELIX 2 2 GLU A 35 GLY A 42 1 8 HELIX 3 3 GLY A 66 PHE A 70 5 5 HELIX 4 4 THR A 74 ARG A 79 1 6 HELIX 5 5 ASP A 92 ALA A 110 1 19 HELIX 6 6 ASP A 132 GLY A 144 1 13 HELIX 7 7 ALA A 155 MET A 173 1 19 HELIX 8 8 THR B 341 LYS B 362 1 22 HELIX 9 9 ASN B 364 LYS B 382 1 19 HELIX 10 10 LYS B 385 ARG B 390 1 6 HELIX 11 11 PRO B 391 SER B 394 5 4 HELIX 12 12 SER B 399 ALA B 420 1 22 HELIX 13 13 THR B 427 LEU B 448 1 22 HELIX 14 14 ASP B 457 LYS B 461 5 5 HELIX 15 15 GLY B 463 ALA B 479 1 17 HELIX 16 16 THR B 490 SER B 507 1 18 HELIX 17 17 ASN B 511 SER B 521 1 11 SHEET 1 A 6 PHE A 45 LEU A 52 0 SHEET 2 A 6 LYS A 55 ASP A 63 -1 O ILE A 57 N ILE A 50 SHEET 3 A 6 TYR A 7 ILE A 14 1 N PHE A 9 O LYS A 58 SHEET 4 A 6 GLY A 83 ASP A 89 1 O ILE A 85 N LEU A 12 SHEET 5 A 6 ASN A 115 ASN A 121 1 O VAL A 119 N VAL A 86 SHEET 6 A 6 PHE A 147 THR A 150 1 O LEU A 148 N GLY A 120 SHEET 1 B 2 LYS B 484 ILE B 485 0 SHEET 2 B 2 HIS B 488 ASN B 489 -1 O HIS B 488 N ILE B 485 SITE 1 AC1 4 GLY A 18 VAL A 19 GLY A 20 SER A 22 CRYST1 100.756 100.756 146.360 90.00 90.00 120.00 P 63 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 0.009925 0.005730 0.000000 0.00000 SCALE2 0.000000 0.011460 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006832 0.00000