3JZ9 - Header Asymmetric Unit

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 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): 592 ; 4.408 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 536 ; 6.344 ; 4.500 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 RCSB ID CODE IS RCSB055346.

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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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. = -3.7 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 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 113 DISTANCE = 5.08 ANGSTROMS

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 REMARK 900 DOMAIN OF 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