HEADER SIGNALING PROTEIN 09-SEP-99 1D06 TITLE STRUCTURAL BASIS OF DIMERIZATION AND SENSORY MECHANISMS OF OXYGEN- TITLE 2 SENSING DOMAIN OF RHIZOBIUM MELILOTI FIXL DETERMINED AT 1.4A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROGEN FIXATION REGULATORY PROTEIN FIXL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SINORHIZOBIUM MELILOTI; SOURCE 3 ORGANISM_TAXID: 382; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET-C KEYWDS OXYGEN SENSOR, HISTIDINE KINASE, PAS, HIGH-RESOLUTION, TWO-COMPONENT KEYWDS 2 SYSTEM, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.MIYATAKE,M.MUKAI,S.-Y.PARK,S.ADACHI,K.TAMURA,H.NAKAMURA,K.NAKAMURA, AUTHOR 2 T.TSUCHIYA,T.IIZUKA,Y.SHIRO REVDAT 7 07-FEB-24 1D06 1 REMARK REVDAT 6 03-NOV-21 1D06 1 REMARK SEQADV REVDAT 5 31-JAN-18 1D06 1 REMARK REVDAT 4 13-JUL-11 1D06 1 VERSN REVDAT 3 24-FEB-09 1D06 1 VERSN REVDAT 2 22-JUL-03 1D06 1 JRNL REVDAT 1 15-MAR-00 1D06 0 JRNL AUTH H.MIYATAKE,M.MUKAI,S.-Y.PARK,S.ADACHI,K.TAMURA,H.NAKAMURA, JRNL AUTH 2 K.NAKAMURA,T.TSUCHIYA,T.IIZUKA,Y.SHIRO JRNL TITL SENSORY MECHANISM OF OXYGEN SENSOR FIXL FROM RHIZOBIUM JRNL TITL 2 MELILOTI: CRYSTALLOGRAPHIC, MUTAGENESIS AND RESONANCE RAMAN JRNL TITL 3 SPECTROSCOPIC STUDIES JRNL REF J.MOL.BIOL. V. 301 415 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10926518 JRNL DOI 10.1006/JMBI.2000.3954 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 21313 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) : 0.224 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1040 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3298 REMARK 3 BIN R VALUE (WORKING SET) : 0.3250 REMARK 3 BIN FREE R VALUE : 0.3440 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 180 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1019 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.23 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.300 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.110 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.140 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.180 ; 2.500 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1D06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-99. REMARK 100 THE DEPOSITION ID IS D_1000009669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR/MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41962 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 22.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, ACETATE BUFFER, PH 4.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 20K, TEMPERATURE REMARK 280 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 30.30000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.57500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.30000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.57500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 37.41626 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 48.75894 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 HIS A 194 CG HIS A 194 CD2 0.067 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 ILE A 209 -30.81 -138.36 REMARK 500 ILE A 212 77.43 -151.10 REMARK 500 VAL A 216 -158.85 -135.95 REMARK 500 SER A 237 115.77 -161.97 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 194 NE2 REMARK 620 2 HEM A 501 NA 99.8 REMARK 620 3 HEM A 501 NB 95.8 88.7 REMARK 620 4 HEM A 501 NC 99.4 160.8 89.3 REMARK 620 5 HEM A 501 ND 101.4 88.9 162.8 87.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 501 DBREF 1D06 A 122 251 UNP P10955 FIXL_RHIME 122 251 SEQADV 1D06 GLY A 122 UNP P10955 ARG 122 ENGINEERED MUTATION SEQADV 1D06 SER A 123 UNP P10955 ARG 123 ENGINEERED MUTATION SEQADV 1D06 HIS A 124 UNP P10955 ALA 124 ENGINEERED MUTATION SEQADV 1D06 MET A 125 UNP P10955 ILE 125 ENGINEERED MUTATION SEQADV 1D06 LEU A 126 UNP P10955 ASP 126 ENGINEERED MUTATION SEQADV 1D06 GLU A 127 UNP P10955 ARG 127 ENGINEERED MUTATION SEQRES 1 A 130 GLY SER HIS MET LEU GLU THR GLU ASP VAL VAL ARG ALA SEQRES 2 A 130 ARG ASP ALA HIS LEU ARG SER ILE LEU ASP THR VAL PRO SEQRES 3 A 130 ASP ALA THR VAL VAL SER ALA THR ASP GLY THR ILE VAL SEQRES 4 A 130 SER PHE ASN ALA ALA ALA VAL ARG GLN PHE GLY TYR ALA SEQRES 5 A 130 GLU GLU GLU VAL ILE GLY GLN ASN LEU ARG ILE LEU MET SEQRES 6 A 130 PRO GLU PRO TYR ARG HIS GLU HIS ASP GLY TYR LEU GLN SEQRES 7 A 130 ARG TYR MET ALA THR GLY GLU LYS ARG ILE ILE GLY ILE SEQRES 8 A 130 ASP ARG VAL VAL SER GLY GLN ARG LYS ASP GLY SER THR SEQRES 9 A 130 PHE PRO MET LYS LEU ALA VAL GLY GLU MET ARG SER GLY SEQRES 10 A 130 GLY GLU ARG PHE PHE THR GLY PHE ILE ARG ASP LEU THR HET HEM A 501 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *73(H2 O) HELIX 1 1 SER A 123 ASP A 136 1 14 HELIX 2 2 HIS A 138 ASP A 144 1 7 HELIX 3 3 ASN A 163 GLY A 171 1 9 HELIX 4 4 ALA A 173 ILE A 178 1 6 HELIX 5 5 LEU A 182 MET A 186 5 5 HELIX 6 6 PRO A 189 GLY A 205 1 17 SHEET 1 A 5 ILE A 159 PHE A 162 0 SHEET 2 A 5 ALA A 149 ALA A 154 -1 O VAL A 152 N VAL A 160 SHEET 3 A 5 GLU A 240 ASP A 249 -1 O PHE A 243 N SER A 153 SHEET 4 A 5 THR A 225 SER A 237 -1 N LYS A 229 O ARG A 248 SHEET 5 A 5 ARG A 214 GLN A 219 -1 O ARG A 214 N LEU A 230 LINK NE2 HIS A 194 FE HEM A 501 1555 1555 2.14 CISPEP 1 GLU A 188 PRO A 189 0 0.34 SITE 1 AC1 24 HOH A 11 HOH A 34 HOH A 56 VAL A 151 SITE 2 AC1 24 LEU A 182 LEU A 185 MET A 186 TYR A 190 SITE 3 AC1 24 HIS A 194 TYR A 197 LEU A 198 TYR A 201 SITE 4 AC1 24 LYS A 207 ARG A 208 ILE A 209 ILE A 210 SITE 5 AC1 24 ARG A 214 VAL A 216 SER A 217 MET A 228 SITE 6 AC1 24 LEU A 230 VAL A 232 PHE A 243 GLY A 245 CRYST1 60.600 37.150 53.990 90.00 115.43 90.00 C 1 2 1 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 0.016502 0.000000 0.007846 0.00000 SCALE2 0.000000 0.026918 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020509 0.00000