HEADER TRANSPORT PROTEIN 23-SEP-09 3JZ9 TITLE CRYSTAL STRUCTURE OF THE GEF DOMAIN OF DRRA/SIDM FROM LEGIONELLA TITLE 2 PNEUMOPHILA COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN DRRA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GEF DOMAIN: UNP RESIDUES 340-533; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA STR. SOURCE 3 PHILADELPHIA 1; SOURCE 4 ORGANISM_TAXID: 272624; SOURCE 5 STRAIN: PHILADELPHIA 1 / DSM 7513; SOURCE 6 ATCC: 33152; SOURCE 7 GENE: LPG2464; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET19MOD_TEV KEYWDS RABGDI, RABGEF, GDI, GEF, GDF, GDI DISPLACEMENT FACTOR, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.SCHOEBEL,L.K.OESTERLIN,W.BLANKENFELDT,R.S.GOODY,A.ITZEN REVDAT 3 01-NOV-17 3JZ9 1 REMARK REVDAT 2 13-JUL-11 3JZ9 1 VERSN REVDAT 1 19-JAN-10 3JZ9 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) : 27.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30721 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1544 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) : 2125 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.91 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 102 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1529 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 27.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.62000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : -0.93000 REMARK 3 B12 (A**2) : 0.31000 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): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.449 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1592 ; 0.034 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1093 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2154 ; 2.304 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2705 ; 1.216 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 208 ; 6.252 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 69 ;36.666 ;25.942 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;15.546 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;26.096 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 243 ; 0.162 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1760 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 283 ; 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): 1000 ; 1.502 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 401 ; 0.538 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1612 ; 2.473 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 592 ; 4.408 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 536 ; 6.344 ; 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 : 1 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 -10 A 9999 REMARK 3 ORIGIN FOR THE GROUP (A): 43.2328 33.1224 0.1269 REMARK 3 T TENSOR REMARK 3 T11: 0.0970 T22: 0.0655 REMARK 3 T33: 0.0601 T12: 0.0711 REMARK 3 T13: -0.0331 T23: -0.0248 REMARK 3 L TENSOR REMARK 3 L11: 1.2947 L22: 1.0886 REMARK 3 L33: 0.1440 L12: -0.7910 REMARK 3 L13: 0.3705 L23: -0.3593 REMARK 3 S TENSOR REMARK 3 S11: 0.0599 S12: 0.0757 S13: -0.1005 REMARK 3 S21: -0.0528 S22: -0.0266 S23: -0.0131 REMARK 3 S31: 0.0472 S32: 0.0329 S33: -0.0333 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 3JZ9 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_1000055346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 1.007490 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 : 30729 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2800 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.5.0070 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.25 M SODIUM SULFATE, 21% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 23.95000 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 11.97500 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 0.00000 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 23.95000 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 11.97500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HOH A 34 LIES ON A SPECIAL POSITION. 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 TYR A 532 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 533 CG 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 O HOH A 194 O HOH A 221 1.73 REMARK 500 CG MSE A 487 O HOH A 219 1.83 REMARK 500 O HOH A 81 O HOH A 178 1.85 REMARK 500 O HOH A 184 O HOH A 208 1.96 REMARK 500 O HOH A 32 O HOH A 222 2.06 REMARK 500 OD1 ASP A 354 O HOH A 106 2.14 REMARK 500 SE MSE A 487 O HOH A 219 2.16 REMARK 500 O HOH A 17 O HOH A 174 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 187 O HOH A 188 4665 1.24 REMARK 500 O HOH A 147 O HOH A 223 1556 1.61 REMARK 500 O HOH A 48 O HOH A 217 4665 1.97 REMARK 500 O HOH A 48 O HOH A 172 4665 2.04 REMARK 500 O HOH A 145 O HOH A 223 1556 2.07 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 MSE A 339 CG MSE A 339 SE -0.341 REMARK 500 GLU A 381 CG GLU A 381 CD 0.095 REMARK 500 ALA A 421 CA ALA A 421 CB 0.146 REMARK 500 THR A 427 C THR A 427 O 0.143 REMARK 500 GLU A 505 CD GLU A 505 OE2 -0.068 REMARK 500 ARG A 506 CZ ARG A 506 NH1 -0.092 REMARK 500 GLU A 528 CG GLU A 528 CD 0.095 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 ARG A 342 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 MSE A 379 CG - SE - CE ANGL. DEV. = -24.2 DEGREES REMARK 500 SER A 417 CA - CB - OG ANGL. DEV. = -17.8 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 SER A 426 21.30 -147.40 REMARK 500 GLU A 452 155.84 136.74 REMARK 500 TRP A 486 -129.32 54.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JZA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN RAB1B IN COMPLEX WITH THE GEF DOMAIN OF REMARK 900 DRRA/SIDM FROM LEGIONELLA PNEUMOPHILA DBREF 3JZ9 A 340 533 UNP Q5ZSQ3 Q5ZSQ3_LEGPH 340 533 SEQADV 3JZ9 GLY A 337 UNP Q5ZSQ3 EXPRESSION TAG SEQADV 3JZ9 HIS A 338 UNP Q5ZSQ3 EXPRESSION TAG SEQADV 3JZ9 MSE A 339 UNP Q5ZSQ3 EXPRESSION TAG SEQRES 1 A 197 GLY HIS MSE VAL THR ARG ILE GLU ASN LEU GLU ASN ALA SEQRES 2 A 197 LYS LYS LEU TRP ASP ASN ALA ASN SER MSE LEU GLU LYS SEQRES 3 A 197 GLY ASN ILE SER GLY TYR LEU LYS ALA ALA ASN GLU LEU SEQRES 4 A 197 HIS LYS PHE MSE LYS GLU LYS ASN LEU LYS GLU ASP ASP SEQRES 5 A 197 LEU ARG PRO GLU LEU SER ASP LYS THR ILE SER PRO LYS SEQRES 6 A 197 GLY TYR ALA ILE LEU GLN SER LEU TRP GLY ALA ALA SER SEQRES 7 A 197 ASP TYR SER ARG ALA ALA ALA THR LEU THR GLU SER THR SEQRES 8 A 197 VAL GLU PRO GLY LEU VAL SER ALA VAL ASN LYS MSE SER SEQRES 9 A 197 ALA PHE PHE MSE ASP CYS LYS LEU SER PRO ASN GLU ARG SEQRES 10 A 197 ALA THR PRO ASP PRO ASP PHE LYS VAL GLY LYS SER LYS SEQRES 11 A 197 ILE LEU VAL GLY ILE MSE GLN PHE ILE LYS ASP VAL ALA SEQRES 12 A 197 ASP PRO THR SER LYS ILE TRP MSE HIS ASN THR LYS ALA SEQRES 13 A 197 LEU MSE ASN HIS LYS ILE ALA ALA ILE GLN LYS LEU GLU SEQRES 14 A 197 ARG SER ASN ASN VAL ASN ASP GLU THR LEU GLU SER VAL SEQRES 15 A 197 LEU SER SER LYS GLY GLU ASN LEU SER GLU TYR LEU SER SEQRES 16 A 197 TYR LYS MODRES 3JZ9 MSE A 339 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 359 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 379 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 439 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 444 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 472 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 487 MET SELENOMETHIONINE MODRES 3JZ9 MSE A 494 MET SELENOMETHIONINE HET MSE A 339 8 HET MSE A 359 8 HET MSE A 379 8 HET MSE A 439 8 HET MSE A 444 8 HET MSE A 472 8 HET MSE A 487 8 HET MSE A 494 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 HOH *225(H2 O) HELIX 1 1 GLY A 337 LYS A 362 1 26 HELIX 2 2 ASN A 364 LYS A 382 1 19 HELIX 3 3 LYS A 385 ARG A 390 1 6 HELIX 4 4 PRO A 391 SER A 394 5 4 HELIX 5 5 SER A 399 ALA A 420 1 22 HELIX 6 6 THR A 427 LEU A 448 1 22 HELIX 7 7 GLY A 463 ALA A 479 1 17 HELIX 8 8 THR A 490 SER A 507 1 18 HELIX 9 9 ASN A 511 SER A 521 1 11 SHEET 1 A 2 LYS A 484 ILE A 485 0 SHEET 2 A 2 HIS A 488 ASN A 489 -1 O HIS A 488 N ILE A 485 LINK C HIS A 338 N MSE A 339 1555 1555 1.36 LINK C MSE A 339 N VAL A 340 1555 1555 1.35 LINK C SER A 358 N MSE A 359 1555 1555 1.31 LINK C MSE A 359 N LEU A 360 1555 1555 1.33 LINK C PHE A 378 N MSE A 379 1555 1555 1.32 LINK C MSE A 379 N LYS A 380 1555 1555 1.34 LINK C LYS A 438 N MSE A 439 1555 1555 1.31 LINK C MSE A 439 N SER A 440 1555 1555 1.33 LINK C PHE A 443 N MSE A 444 1555 1555 1.33 LINK C MSE A 444 N ASP A 445 1555 1555 1.32 LINK C ILE A 471 N MSE A 472 1555 1555 1.33 LINK C MSE A 472 N GLN A 473 1555 1555 1.32 LINK C TRP A 486 N MSE A 487 1555 1555 1.31 LINK C MSE A 487 N HIS A 488 1555 1555 1.35 LINK C LEU A 493 N MSE A 494 1555 1555 1.31 LINK C MSE A 494 N ASN A 495 1555 1555 1.34 CRYST1 126.338 126.338 35.925 90.00 90.00 120.00 P 62 6 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 0.007915 0.004570 0.000000 0.00000 SCALE2 0.000000 0.009140 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027836 0.00000