HEADER OXYGEN STORAGE/TRANSPORT 31-AUG-05 2AWC TITLE DEOXY-DCRH-HR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMERYTHRIN-LIKE DOMAIN PROTEIN DCRH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DESULFOVIBRIO VULGARIS; SOURCE 3 ORGANISM_TAXID: 881; 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: PDVHR KEYWDS FOUR HELIX BUNDLE, OXYGEN STORAGE-TRANSPORT COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.E.ISAZA,R.SILAGHI-DUMITRESCU,R.B.IYER,D.M.KURTZ,M.K.CHAN REVDAT 3 14-FEB-24 2AWC 1 REMARK LINK REVDAT 2 24-FEB-09 2AWC 1 VERSN REVDAT 1 15-AUG-06 2AWC 0 JRNL AUTH C.E.ISAZA,R.SILAGHI-DUMITRESCU,R.B.IYER,D.M.KURTZ,M.K.CHAN JRNL TITL STRUCTURAL BASIS FOR O(2) SENSING BY THE HEMERYTHRIN-LIKE JRNL TITL 2 DOMAIN OF A BACTERIAL CHEMOTAXIS PROTEIN: SUBSTRATE TUNNEL JRNL TITL 3 AND FLUXIONAL N TERMINUS JRNL REF BIOCHEMISTRY V. 45 9023 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16866347 JRNL DOI 10.1021/BI0607812 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1522048.190 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 6537 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) : 0.204 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 712 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 879 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 106 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1100 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 54 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 16.80000 REMARK 3 B22 (A**2) : -6.02000 REMARK 3 B33 (A**2) : -10.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -7.59000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 17.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.320 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.970 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.110 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 63.21 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 : IONZ_SWAP.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 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.984 REMARK 200 MONOCHROMATOR : CURVED CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : MOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.09000 REMARK 200 FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : 0.34400 REMARK 200 FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: K2PT(CN)4 , TRIS-HCL, PEG 3350, CACL2, REMARK 280 ISOPROPANOL, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 16.56000 REMARK 290 SMTRY3 2 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: 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 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 LYS A 8 173.97 -57.45 REMARK 500 SER A 10 -179.74 -58.74 REMARK 500 ALA A 14 160.42 -46.66 REMARK 500 ASN A 15 -153.09 -174.10 REMARK 500 ASN A 15 -157.56 -146.70 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 FEO A 137 FE2 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 23 NE2 REMARK 620 2 FEO A 137 O 147.9 REMARK 620 3 HIS A 59 NE2 83.9 95.5 REMARK 620 4 GLU A 63 OE2 118.8 93.4 91.4 REMARK 620 5 ASP A 123 OD2 85.9 93.9 169.8 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FEO A 137 FE1 REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE1 REMARK 620 2 FEO A 137 O 89.9 REMARK 620 3 HIS A 78 NE2 86.2 175.8 REMARK 620 4 HIS A 82 NE2 85.8 94.6 83.5 REMARK 620 5 HIS A 118 NE2 177.0 88.8 95.0 91.6 REMARK 620 6 ASP A 123 OD1 89.4 95.2 86.4 169.1 93.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FEO A 137 DBREF 2AWC A 7 136 UNP Q9REU3 Q9REU3_DESVU 7 136 SEQRES 1 A 130 VAL LYS TRP SER GLU ASP LEU ALA ASN LEU PRO SER ILE SEQRES 2 A 130 ASP THR GLN HIS LYS ARG LEU VAL ASP TYR ILE ASN ASP SEQRES 3 A 130 LEU TYR ARG ALA ALA ARG ARG ARG ASP MET ASP LYS ALA SEQRES 4 A 130 ARG GLU VAL PHE ASP ALA LEU LYS ASN TYR ALA VAL GLU SEQRES 5 A 130 HIS PHE GLY TYR GLU GLU ARG LEU PHE ALA ASP TYR ALA SEQRES 6 A 130 TYR PRO GLU ALA THR ARG HIS LYS GLU ILE HIS ARG ARG SEQRES 7 A 130 PHE VAL GLU THR VAL LEU LYS TRP GLU LYS GLN LEU ALA SEQRES 8 A 130 ALA GLY ASP PRO GLU VAL VAL MET THR THR LEU ARG GLY SEQRES 9 A 130 LEU VAL ASP TRP LEU VAL ASN HIS ILE MET LYS GLU ASP SEQRES 10 A 130 LYS LYS TYR GLU ALA TYR LEU ARG GLU ARG GLY VAL SER HET FEO A 137 3 HETNAM FEO MU-OXO-DIIRON FORMUL 2 FEO FE2 O FORMUL 3 HOH *54(H2 O) HELIX 1 1 LEU A 16 ARG A 39 1 24 HELIX 2 2 ASP A 41 TYR A 70 1 30 HELIX 3 3 GLU A 74 LEU A 96 1 23 HELIX 4 4 ASP A 100 GLU A 122 1 23 HELIX 5 5 ASP A 123 LYS A 125 5 3 HELIX 6 6 TYR A 126 GLU A 132 1 7 LINK NE2 HIS A 23 FE2 FEO A 137 1555 1555 2.11 LINK NE2 HIS A 59 FE2 FEO A 137 1555 1555 2.19 LINK OE1 GLU A 63 FE1 FEO A 137 1555 1555 2.33 LINK OE2 GLU A 63 FE2 FEO A 137 1555 1555 2.22 LINK NE2 HIS A 78 FE1 FEO A 137 1555 1555 2.25 LINK NE2 HIS A 82 FE1 FEO A 137 1555 1555 2.11 LINK NE2 HIS A 118 FE1 FEO A 137 1555 1555 2.15 LINK OD1 ASP A 123 FE1 FEO A 137 1555 1555 2.18 LINK OD2 ASP A 123 FE2 FEO A 137 1555 1555 2.06 SITE 1 AC1 7 HIS A 23 HIS A 59 GLU A 63 HIS A 78 SITE 2 AC1 7 HIS A 82 HIS A 118 ASP A 123 CRYST1 43.980 33.120 44.700 90.00 96.02 90.00 P 1 21 1 2 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 0.022738 0.000000 0.002398 0.00000 SCALE2 0.000000 0.030193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022495 0.00000