HEADER OXYGEN STORAGE/TRANSPORT 22-SEP-98 1BV5 OBSLTE 24-JAN-00 1BV5 1DRQ TITLE CRYSTAL STRUCTURE OF FIXL HEME DOMAIN COMPLEXED WITH CN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (HISTIDINE KINASE); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HEME DOMAIN SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRADYRHIZOBIUM JAPONICUM KEYWDS FIXL, HEME, HISTIDINE KINASE, SIGNAL TRANSDUCTION EXPDTA X-RAY DIFFRACTION AUTHOR W.GONG,B.HAO,S.S.MANSY,G.GONZALEZ,M.A.GILLES-GONZALEZ, AUTHOR 2 M.K.CHAN REVDAT 3 24-JAN-00 1BV5 1 OBSLTE REVDAT 2 12-JAN-00 1BV5 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 23-DEC-98 1BV5 0 JRNL AUTH W.GONG,B.HAO,S.S.MANSY,G.GONZALEZ, JRNL AUTH 2 M.A.GILLES-GONZALEZ,M.K.CHAN JRNL TITL STRUCTURE OF A BIOLOGICAL OXYGEN SENSOR: A NEW JRNL TITL 2 MECHANISM FOR HEME-DRIVEN SIGNAL TRANSDUCTION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 95 15177 1998 JRNL REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 2.70 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.7 REMARK 3 NUMBER OF REFLECTIONS : 4480 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400 REMARK 3 FREE R VALUE TEST SET COUNT : 389 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 535 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 51 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 : 930 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 51 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.68 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 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 1BV5 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-JUN-1999. REMARK 100 THE RCSB ID CODE IS RCSB008328. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.6984 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4402 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.04900 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) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21500 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: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.0 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 2/3+X,1/3+Y,1/3+Z REMARK 290 8555 2/3-Y,1/3+X-Y,1/3+Z REMARK 290 9555 2/3-X+Y,1/3-X,1/3+Z REMARK 290 10555 2/3+Y,1/3+X,1/3-Z REMARK 290 11555 2/3+X-Y,1/3-Y,1/3-Z REMARK 290 12555 2/3-X,1/3-X+Y,1/3-Z REMARK 290 13555 1/3+X,2/3+Y,2/3+Z REMARK 290 14555 1/3-Y,2/3+X-Y,2/3+Z REMARK 290 15555 1/3-X+Y,2/3-X,2/3+Z REMARK 290 16555 1/3+Y,2/3+X,2/3-Z REMARK 290 17555 1/3+X-Y,2/3-Y,2/3-Z REMARK 290 18555 1/3-X,2/3-X+Y,2/3-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 -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 64.25500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.09764 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 19.79333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 64.25500 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 37.09764 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.79333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 64.25500 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 37.09764 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 19.79333 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 64.25500 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 37.09764 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 19.79333 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 64.25500 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 37.09764 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 19.79333 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 64.25500 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 37.09764 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 19.79333 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 74.19528 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 39.58667 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 74.19528 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 39.58667 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 74.19528 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 39.58667 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 74.19528 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 39.58667 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 74.19528 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 39.58667 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 74.19528 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 39.58667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 HIS A 4 REMARK 465 LEU A 5 REMARK 465 ARG A 6 REMARK 465 SER A 7 REMARK 465 ILE A 8 REMARK 465 LEU A 9 REMARK 465 HIS A 10 REMARK 465 THR A 11 REMARK 465 ILE A 12 REMARK 465 PRO A 13 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 REMARK 500 FE HEM 719 C1 CN 500 2.02 REMARK 500 NE2 HIS A 60 FE HEM 719 2.05 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 44 N - CA - C ANGL. DEV. = 10.3 DEGREES REMARK 500 ASN A 49 CB - CA - C ANGL. DEV. =-12.1 DEGREES REMARK 500 LEU A 96 CA - CB - CG ANGL. DEV. = 10.7 DEGREES DBREF 1BV5 A 1 130 UNP P23222 FIXL_BRAJA 141 270 SEQRES 1 A 130 ARG GLU THR HIS LEU ARG SER ILE LEU HIS THR ILE PRO SEQRES 2 A 130 ASP ALA MET ILE VAL ILE ASP GLY HIS GLY ILE ILE GLN SEQRES 3 A 130 LEU PHE SER THR ALA ALA GLU ARG LEU PHE GLY TRP SER SEQRES 4 A 130 GLU LEU GLU ALA ILE GLY GLN ASN VAL ASN ILE LEU MET SEQRES 5 A 130 PRO GLU PRO ASP ARG SER ARG HIS ASP SER TYR ILE SER SEQRES 6 A 130 ARG TYR ARG THR THR SER ASP PRO HIS ILE ILE GLY ILE SEQRES 7 A 130 GLY ARG ILE VAL THR GLY LYS ARG ARG ASP GLY THR THR SEQRES 8 A 130 PHE PRO MET HIS LEU SER ILE GLY GLU MET GLN SER GLY SEQRES 9 A 130 GLY GLU PRO TYR PHE THR GLY PHE VAL ARG ASP LEU THR SEQRES 10 A 130 GLU HIS GLN GLN THR GLN ALA ARG LEU GLN GLU LEU GLN HET HEM 719 43 HET CN 500 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CN CYANIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 CN C H N FORMUL 4 HOH *51(H2 O1) HELIX 1 1 THR A 30 PHE A 36 1 7 HELIX 2 2 GLU A 40 ILE A 44 1 5 HELIX 3 3 VAL A 48 LEU A 51 5 4 HELIX 4 4 ASP A 56 THR A 70 1 15 HELIX 5 5 THR A 117 GLU A 128 1 12 SHEET 1 A 5 ARG A 80 LYS A 85 0 SHEET 2 A 5 THR A 91 SER A 103 -1 N LEU A 96 O ARG A 80 SHEET 3 A 5 GLU A 106 ASP A 115 -1 N ARG A 114 O HIS A 95 SHEET 4 A 5 ALA A 15 ILE A 19 -1 N ILE A 19 O PHE A 109 SHEET 5 A 5 ILE A 25 PHE A 28 -1 N LEU A 27 O VAL A 18 CISPEP 1 GLU A 54 PRO A 55 0 -0.20 CRYST1 128.510 128.510 59.380 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 0.007781 0.004493 0.000000 0.00000 SCALE2 0.000000 0.008985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016841 0.00000