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- PDB-8avi: Crystal structure of IsdG from Bacillus cereus in complex with heme -

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Basic information

Entry
Database: PDB / ID: 8avi
TitleCrystal structure of IsdG from Bacillus cereus in complex with heme
ComponentsHeme-degrading monooxygenase
KeywordsOXIDOREDUCTASE / HEME DEGRADATION / MONOOXYGENASE
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / iron import into cell / heme oxygenase (decyclizing) activity / heme catabolic process / iron ion binding / heme binding / cytoplasm
Similarity search - Function
Heme oxygenase IsdG / : / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel
Similarity search - Domain/homology
1,4-BUTANEDIOL / PROTOPORPHYRIN IX CONTAINING FE / 1,3-PROPANDIOL / S-1,2-PROPANEDIOL / Heme-degrading monooxygenase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAndersen, H.K. / Hammerstad, M. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway301584 Norway
CitationJournal: Antioxidants / Year: 2023
Title: Functional Diversity of Homologous Oxidoreductases-Tuning of Substrate Specificity by a FAD-Stacking Residue for Iron Acquisition and Flavodoxin Reduction.
Authors: Hammerstad, M. / Rugtveit, A.K. / Dahlen, S. / Andersen, H.K. / Hersleth, H.P.
History
DepositionAug 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-degrading monooxygenase
B: Heme-degrading monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5757
Polymers24,1002
Non-polymers1,4755
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-41 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.703, 48.941, 100.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Heme-degrading monooxygenase / Heme oxygenase / Iron-regulated surface determinant / Iron-responsive surface determinant


Mass: 12049.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria)
Strain: ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711
Gene: isdG, BC_4542 / Plasmid: pET22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q812Q3, heme oxygenase (staphylobilin-producing)

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Non-polymers , 5 types, 47 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18 mg/mL IsdaG (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0. ...Details: 18 mg/mL IsdaG (1:1) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.02 M 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M (RS)-1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.969998 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969998 Å / Relative weight: 1
ReflectionResolution: 2→44.04 Å / Num. obs: 16227 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1200 / CC1/2: 0.579 / Rpim(I) all: 0.498 / Rrim(I) all: 1.313 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AVH

8avh


Resolution: 2→44.04 Å / SU ML: 0.2365 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.5781
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 853 5.27 %
Rwork0.2005 15324 -
obs0.2024 16177 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.14 Å2
Refinement stepCycle: LAST / Resolution: 2→44.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 102 42 1816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761885
X-RAY DIFFRACTIONf_angle_d0.93542581
X-RAY DIFFRACTIONf_chiral_restr0.0573269
X-RAY DIFFRACTIONf_plane_restr0.0065318
X-RAY DIFFRACTIONf_dihedral_angle_d15.2318672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.32241510.27522510X-RAY DIFFRACTION100
2.13-2.290.29721500.25012492X-RAY DIFFRACTION99.92
2.29-2.520.25541610.21922517X-RAY DIFFRACTION100
2.52-2.880.27321230.22572561X-RAY DIFFRACTION100
2.88-3.630.28691370.21892582X-RAY DIFFRACTION99.78
3.63-44.040.1961310.17642662X-RAY DIFFRACTION97.79

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