HEADER OXIDOREDUCTASE 26-AUG-22 8AVI TITLE CRYSTAL STRUCTURE OF ISDG FROM BACILLUS CEREUS IN COMPLEX WITH HEME COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME-DEGRADING MONOOXYGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HEME OXYGENASE,IRON-REGULATED SURFACE DETERMINANT,IRON- COMPND 5 RESPONSIVE SURFACE DETERMINANT; COMPND 6 EC: 1.14.99.48; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CEREUS ATCC 14579; SOURCE 3 ORGANISM_TAXID: 226900; SOURCE 4 STRAIN: ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / SOURCE 5 NCIMB 9373 / NCTC 2599 / NRRL B-3711; SOURCE 6 GENE: ISDG, BC_4542; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS HEME DEGRADATION, MONOOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.K.ANDERSEN,M.HAMMERSTAD,H.-P.HERSLETH REVDAT 2 07-FEB-24 8AVI 1 REMARK REVDAT 1 12-JUL-23 8AVI 0 JRNL AUTH M.HAMMERSTAD,A.K.RUGTVEIT,S.DAHLEN,H.K.ANDERSEN,H.P.HERSLETH JRNL TITL FUNCTIONAL DIVERSITY OF HOMOLOGOUS OXIDOREDUCTASES-TUNING OF JRNL TITL 2 SUBSTRATE SPECIFICITY BY A FAD-STACKING RESIDUE FOR IRON JRNL TITL 3 ACQUISITION AND FLAVODOXIN REDUCTION. JRNL REF ANTIOXIDANTS V. 12 2023 JRNL REFN ESSN 2076-3921 JRNL PMID 37371954 JRNL DOI 10.3390/ANTIOX12061224 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16177 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 853 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.0400 - 3.6300 0.98 2662 131 0.1764 0.1960 REMARK 3 2 3.6300 - 2.8800 1.00 2582 137 0.2189 0.2869 REMARK 3 3 2.8800 - 2.5200 1.00 2561 123 0.2257 0.2732 REMARK 3 4 2.5200 - 2.2900 1.00 2517 161 0.2192 0.2554 REMARK 3 5 2.2900 - 2.1300 1.00 2492 150 0.2501 0.2972 REMARK 3 6 2.1300 - 2.0000 1.00 2510 151 0.2752 0.3224 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.237 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.578 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.14 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 1885 REMARK 3 ANGLE : 0.935 2581 REMARK 3 CHIRALITY : 0.057 269 REMARK 3 PLANARITY : 0.007 318 REMARK 3 DIHEDRAL : 15.232 672 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8AVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125162. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX IV REMARK 200 BEAMLINE : BIOMAX REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.969998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16227 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 44.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 1.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 8AVH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18 MG/ML ISDAG (1:1) 12.5% W/V PEG REMARK 280 1000, 12.5% W/V PEG 3350, 12.5% V/V MPD, 0.02 M 1,6-HEXANEDIOL, REMARK 280 0.02 M 1-BUTANOL, 0.02 M (RS)-1,2-PROPANEDIOL, 0.02 M 2-PROPANOL, REMARK 280 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 0.1 M MOPS/HEPES- REMARK 280 NA PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 23.35150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.46550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.47050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.46550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.35150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.47050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 GLN A 107 REMARK 465 GLN B 107 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 VAL A 46 -71.20 -78.63 REMARK 500 SER A 77 -81.91 -99.92 REMARK 500 VAL B 46 -70.75 -83.66 REMARK 500 HIS B 78 -93.05 51.11 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 B 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 76 NE2 REMARK 620 2 HEM B 200 NA 79.2 REMARK 620 3 HEM B 200 NB 69.9 88.5 REMARK 620 4 HEM B 200 NC 92.8 172.0 89.2 REMARK 620 5 HEM B 200 ND 99.7 90.0 169.6 90.9 REMARK 620 N 1 2 3 4 DBREF 8AVI A 1 107 UNP Q812Q3 HDOX_BACCR 1 107 DBREF 8AVI B 1 107 UNP Q812Q3 HDOX_BACCR 1 107 SEQRES 1 A 107 MET ILE ILE VAL THR ASN THR ALA LYS ILE THR LYS GLY SEQRES 2 A 107 ASN GLY HIS LYS LEU ILE GLU ARG PHE ASN LYS VAL GLY SEQRES 3 A 107 LYS VAL GLU THR MET PRO GLY PHE LEU GLY LEU GLU VAL SEQRES 4 A 107 LEU LEU THR GLN ASN THR VAL ASP TYR ASP GLU VAL THR SEQRES 5 A 107 ILE SER THR ARG TRP ASN ALA LYS GLU ASP PHE GLN GLY SEQRES 6 A 107 TRP THR LYS SER ALA ALA PHE LYS ASP ALA HIS SER HIS SEQRES 7 A 107 GLN GLY GLY MET PRO GLU TYR ILE LEU ASP ASN LYS ILE SEQRES 8 A 107 ALA TYR TYR ASP VAL LYS VAL VAL ARG MET PRO MET ALA SEQRES 9 A 107 ALA ALA GLN SEQRES 1 B 107 MET ILE ILE VAL THR ASN THR ALA LYS ILE THR LYS GLY SEQRES 2 B 107 ASN GLY HIS LYS LEU ILE GLU ARG PHE ASN LYS VAL GLY SEQRES 3 B 107 LYS VAL GLU THR MET PRO GLY PHE LEU GLY LEU GLU VAL SEQRES 4 B 107 LEU LEU THR GLN ASN THR VAL ASP TYR ASP GLU VAL THR SEQRES 5 B 107 ILE SER THR ARG TRP ASN ALA LYS GLU ASP PHE GLN GLY SEQRES 6 B 107 TRP THR LYS SER ALA ALA PHE LYS ASP ALA HIS SER HIS SEQRES 7 B 107 GLN GLY GLY MET PRO GLU TYR ILE LEU ASP ASN LYS ILE SEQRES 8 B 107 ALA TYR TYR ASP VAL LYS VAL VAL ARG MET PRO MET ALA SEQRES 9 B 107 ALA ALA GLN HET HEM A 201 43 HET PGO A 202 5 HET BU1 A 203 6 HET HEM B 200 43 HET PDO B 201 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PGO S-1,2-PROPANEDIOL HETNAM BU1 1,4-BUTANEDIOL HETNAM PDO 1,3-PROPANDIOL HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 PGO C3 H8 O2 FORMUL 5 BU1 C4 H10 O2 FORMUL 7 PDO C3 H8 O2 FORMUL 8 HOH *42(H2 O) HELIX 1 AA1 ASN A 14 ASN A 23 1 10 HELIX 2 AA2 LYS A 27 MET A 31 5 5 HELIX 3 AA3 ALA A 59 SER A 69 1 11 HELIX 4 AA4 SER A 69 ALA A 75 1 7 HELIX 5 AA5 ASN B 14 ASN B 23 1 10 HELIX 6 AA6 LYS B 27 MET B 31 5 5 HELIX 7 AA7 ALA B 59 LYS B 68 1 10 HELIX 8 AA8 SER B 69 HIS B 76 1 8 SHEET 1 AA1 9 ILE A 2 THR A 11 0 SHEET 2 AA1 9 TYR A 48 TRP A 57 -1 O ASP A 49 N ILE A 10 SHEET 3 AA1 9 PHE A 34 THR A 42 -1 N GLU A 38 O SER A 54 SHEET 4 AA1 9 ILE B 86 ARG B 100 -1 O ARG B 100 N LEU A 37 SHEET 5 AA1 9 ILE B 2 THR B 11 -1 N THR B 7 O LYS B 90 SHEET 6 AA1 9 TYR B 48 TRP B 57 -1 O VAL B 51 N ALA B 8 SHEET 7 AA1 9 PHE B 34 THR B 42 -1 N LEU B 35 O ARG B 56 SHEET 8 AA1 9 ILE A 86 ARG A 100 -1 N LYS A 97 O VAL B 39 SHEET 9 AA1 9 ILE A 2 THR A 11 -1 N THR A 7 O LYS A 90 LINK NE2 HIS B 76 FE HEM B 200 1555 1555 2.64 CRYST1 46.703 48.941 100.931 90.00 90.00 90.00 P 21 21 21 8 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 0.021412 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009908 0.00000