HEADER SIGNALING PROTEIN 20-OCT-04 1XT0 TITLE THE STRUCTURE OF N-TERMINAL SEC7 DOMAIN OF RALF COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANINE NUCLEOTIDE EXCHANGE PROTEIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA; SOURCE 3 ORGANISM_TAXID: 446; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHIS-1 KEYWDS THE N-TERMINAL SEC7 DOMAIN OF RALF, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.C.AMOR,J.SWAILS,C.R.ROY,H.NAGAI,A.INGMUNDSON,X.CHENG,R.A.KAHN REVDAT 5 15-NOV-23 1XT0 1 REMARK REVDAT 4 23-AUG-23 1XT0 1 SEQADV LINK REVDAT 3 24-FEB-09 1XT0 1 VERSN REVDAT 2 19-APR-05 1XT0 1 JRNL REVDAT 1 02-NOV-04 1XT0 0 JRNL AUTH J.C.AMOR,J.SWAILS,X.ZHU,C.R.ROY,H.NAGAI,A.INGMUNDSON, JRNL AUTH 2 X.CHENG,R.A.KAHN JRNL TITL THE STRUCTURE OF RALF, AN ADP-RIBOSYLATION FACTOR GUANINE JRNL TITL 2 NUCLEOTIDE EXCHANGE FACTOR FROM LEGIONELLA PNEUMOPHILA, JRNL TITL 3 REVEALS THE PRESENCE OF A CAP OVER THE ACTIVE SITE JRNL REF J.BIOL.CHEM. V. 280 1392 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15520000 JRNL DOI 10.1074/JBC.M410820200 REMARK 2 REMARK 2 RESOLUTION. 2.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 582242.400 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 17589 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 SET) : 0.215 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1645 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.24 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1550 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE : 0.3090 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 166 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1617 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.72800 REMARK 3 B22 (A**2) : -3.58800 REMARK 3 B33 (A**2) : -11.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.33 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 18.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.397 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.108 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.530 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.745 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 47.08 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XT0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-03 REMARK 200 TEMPERATURE (KELVIN) : 108 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17589 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.160 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1XSZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG2K, PH 8.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 20.09750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.56600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.62200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.56600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.09750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.62200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 LYS B 99 N - CA - C ANGL. DEV. = -17.4 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 GLN B 85 123.87 173.86 REMARK 500 ASN B 122 59.22 -142.49 REMARK 500 ASN B 170 69.07 -103.93 REMARK 500 LYS B 198 -159.63 -87.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XSZ RELATED DB: PDB REMARK 900 THE STRUCTURE OF FULL LENGTH RALF DBREF 1XT0 B 2 201 UNP Q8RT31 Q8RT31_LEGPN 2 201 SEQADV 1XT0 GLY B -1 UNP Q8RT31 CLONING ARTIFACT SEQADV 1XT0 ALA B 0 UNP Q8RT31 CLONING ARTIFACT SEQADV 1XT0 SER B 1 UNP Q8RT31 CLONING ARTIFACT SEQADV 1XT0 MSE B 80 UNP Q8RT31 MET 80 MODIFIED RESIDUE SEQADV 1XT0 MSE B 141 UNP Q8RT31 MET 141 MODIFIED RESIDUE SEQADV 1XT0 MSE B 157 UNP Q8RT31 MET 157 MODIFIED RESIDUE SEQRES 1 B 203 GLY ALA SER HIS PRO GLU ILE GLU LYS ALA GLN ARG GLU SEQRES 2 B 203 ILE ILE GLU ALA PHE ASN ALA LYS PRO LYS ASN GLY ILE SEQRES 3 B 203 ASN LYS ILE LYS GLU ILE CYS GLU GLN TYR LYS ILE SER SEQRES 4 B 203 PRO ASN GLU GLU ILE ALA GLU PHE PHE HIS GLN GLN ARG SEQRES 5 B 203 LYS ASN LEU ASP LEU GLU ALA VAL GLY ASP TYR LEU SER SEQRES 6 B 203 SER PRO GLU ALA GLU ASN GLN GLN VAL LEU LYS ALA PHE SEQRES 7 B 203 THR SER GLN MSE ASN PHE ASN GLY GLN SER PHE VAL GLU SEQRES 8 B 203 GLY LEU ARG THR PHE LEU LYS THR PHE LYS LEU PRO GLY SEQRES 9 B 203 GLU ALA GLN LYS ILE ASP ARG LEU VAL GLN SER PHE SER SEQRES 10 B 203 GLY ALA TYR PHE GLN GLN ASN PRO ASP VAL VAL SER ASN SEQRES 11 B 203 ALA ASP ALA ALA TYR LEU LEU ALA PHE GLN THR ILE MSE SEQRES 12 B 203 LEU ASN THR ASP LEU HIS ASN PRO SER ILE PRO GLU LYS SEQRES 13 B 203 ASN LYS MSE THR VAL ASP GLY LEU LYS ARG ASN LEU ARG SEQRES 14 B 203 GLY GLY ASN ASN GLY GLY ASP PHE ASP ALA LYS PHE LEU SEQRES 15 B 203 GLU GLU LEU TYR SER GLU ILE LYS ALA LYS PRO PHE GLU SEQRES 16 B 203 LEU ASN PHE VAL LYS THR SER PRO MODRES 1XT0 MSE B 80 MET SELENOMETHIONINE MODRES 1XT0 MSE B 141 MET SELENOMETHIONINE MODRES 1XT0 MSE B 157 MET SELENOMETHIONINE HET MSE B 80 8 HET MSE B 141 8 HET MSE B 157 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *73(H2 O) HELIX 1 1 HIS B 2 ALA B 8 1 7 HELIX 2 2 ALA B 8 LYS B 19 1 12 HELIX 3 3 LYS B 19 TYR B 34 1 16 HELIX 4 4 SER B 37 GLN B 49 1 13 HELIX 5 5 ARG B 50 LEU B 53 5 4 HELIX 6 6 ASP B 54 SER B 63 1 10 HELIX 7 7 GLU B 66 GLN B 79 1 14 HELIX 8 8 SER B 86 PHE B 98 1 13 HELIX 9 9 GLU B 103 ASN B 122 1 20 HELIX 10 10 ASN B 128 LEU B 146 1 19 HELIX 11 11 PRO B 152 LYS B 156 5 5 HELIX 12 12 THR B 158 LEU B 166 1 9 HELIX 13 13 ASP B 176 LYS B 190 1 15 LINK C GLN B 79 N MSE B 80 1555 1555 1.33 LINK C MSE B 80 N ASN B 81 1555 1555 1.33 LINK C ILE B 140 N MSE B 141 1555 1555 1.33 LINK C MSE B 141 N LEU B 142 1555 1555 1.33 LINK C LYS B 156 N MSE B 157 1555 1555 1.33 LINK C MSE B 157 N THR B 158 1555 1555 1.33 CRYST1 40.195 43.244 109.132 90.00 90.00 90.00 P 21 21 21 4 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 0.024879 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023125 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009163 0.00000