HEADER SIGNALING PROTEIN, TRANSFERASE 22-SEP-04 1XJ3 TITLE BJFIXLH IN UNLIGANDED FERROUS FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENSOR PROTEIN FIXL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEME DOMAIN; COMPND 5 SYNONYM: BJFIXLH FIXL; COMPND 6 EC: 2.7.3.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: REDUCED, UNLIGANDED FORM SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM; SOURCE 3 ORGANISM_TAXID: 375; SOURCE 4 GENE: FIXL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PAS DOMAIN; HEME; OXYGEN SENSOR, SIGNALING PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.KEY,K.MOFFAT REVDAT 3 23-AUG-23 1XJ3 1 REMARK LINK REVDAT 2 24-FEB-09 1XJ3 1 VERSN REVDAT 1 29-MAR-05 1XJ3 0 JRNL AUTH J.KEY,K.MOFFAT JRNL TITL CRYSTAL STRUCTURES OF DEOXY AND CO-BOUND BJFIXLH REVEAL JRNL TITL 2 DETAILS OF LIGAND RECOGNITION AND SIGNALING JRNL REF BIOCHEMISTRY V. 44 4627 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15779889 JRNL DOI 10.1021/BI047942R REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 13604 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) : 0.214 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1345 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.630 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 1XJ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13604 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 200 DATA REDUNDANCY : 16.29 REMARK 200 R MERGE (I) : 0.03100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1DRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, PEI, CAPSO, PH 9.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 64.32200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.13632 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.56500 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 64.32200 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.13632 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.56500 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 64.32200 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.13632 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 19.56500 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 64.32200 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 37.13632 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 19.56500 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 64.32200 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 37.13632 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 19.56500 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 64.32200 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 37.13632 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 19.56500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 74.27265 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 39.13000 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 74.27265 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 39.13000 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 74.27265 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 39.13000 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 74.27265 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 39.13000 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 74.27265 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 39.13000 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 74.27265 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 39.13000 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: 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 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 719 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 200 NE2 REMARK 620 2 HEM A 719 NA 96.5 REMARK 620 3 HEM A 719 NB 93.9 90.3 REMARK 620 4 HEM A 719 NC 95.3 167.9 86.1 REMARK 620 5 HEM A 719 ND 92.5 89.6 173.6 92.6 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 719 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XJ2 RELATED DB: PDB REMARK 900 RELATED ID: 1XJ4 RELATED DB: PDB REMARK 900 RELATED ID: 1XJ6 RELATED DB: PDB DBREF 1XJ3 A 154 269 UNP P23222 FIXL_BRAJA 154 269 SEQRES 1 A 116 ASP ALA MET ILE VAL ILE ASP GLY HIS GLY ILE ILE GLN SEQRES 2 A 116 LEU PHE SER THR ALA ALA GLU ARG LEU PHE GLY TRP SER SEQRES 3 A 116 GLU LEU GLU ALA ILE GLY GLN ASN VAL ASN ILE LEU MET SEQRES 4 A 116 PRO GLU PRO ASP ARG SER ARG HIS ASP SER TYR ILE SER SEQRES 5 A 116 ARG TYR ARG THR THR SER ASP PRO HIS ILE ILE GLY ILE SEQRES 6 A 116 GLY ARG ILE VAL THR GLY LYS ARG ARG ASP GLY THR THR SEQRES 7 A 116 PHE PRO MET HIS LEU SER ILE GLY GLU MET GLN SER GLY SEQRES 8 A 116 GLY GLU PRO TYR PHE THR GLY PHE VAL ARG ASP LEU THR SEQRES 9 A 116 GLU HIS GLN GLN THR GLN ALA ARG LEU GLN GLU LEU HET HEM A 719 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *81(H2 O) HELIX 1 1 SER A 169 GLY A 177 1 9 HELIX 2 2 SER A 179 ILE A 184 1 6 HELIX 3 3 ASN A 187 MET A 192 5 6 HELIX 4 4 PRO A 195 SER A 211 1 17 HELIX 5 5 LEU A 256 LEU A 269 1 14 SHEET 1 A 5 ILE A 165 PHE A 168 0 SHEET 2 A 5 MET A 156 ASP A 160 -1 N VAL A 158 O GLN A 166 SHEET 3 A 5 GLU A 246 ASP A 255 -1 O GLY A 251 N ILE A 157 SHEET 4 A 5 THR A 231 SER A 243 -1 N MET A 241 O TYR A 248 SHEET 5 A 5 ARG A 220 LYS A 225 -1 N GLY A 224 O PHE A 232 LINK NE2 HIS A 200 FE HEM A 719 1555 1555 2.00 CISPEP 1 GLU A 194 PRO A 195 0 -0.14 SITE 1 AC1 19 HOH A 93 HOH A 138 ILE A 159 VAL A 188 SITE 2 AC1 19 LEU A 191 MET A 192 HIS A 200 TYR A 203 SITE 3 AC1 19 PRO A 213 HIS A 214 ILE A 215 ILE A 216 SITE 4 AC1 19 ARG A 220 THR A 223 LEU A 236 ILE A 238 SITE 5 AC1 19 PHE A 249 THR A 250 GLY A 251 CRYST1 128.644 128.644 58.695 90.00 90.00 120.00 H 3 2 18 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 0.007773 0.004488 0.000000 0.00000 SCALE2 0.000000 0.008976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017037 0.00000