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- PDB-9fvs: Crystal structure of Heme-Oxygenase mutant G139A from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 9fvs
TitleCrystal structure of Heme-Oxygenase mutant G139A from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))
Componentsheme oxygenase (biliverdin-producing)
KeywordsOXIDOREDUCTASE / carbon dioxide photoreduction artificial enzyme cobalt-porphyrin heme-oxygenase oxidoreductase
Function / homology
Function and homology information


heme oxygenase (biliverdin-producing) / heme oxidation / heme oxygenase (decyclizing) activity / heme catabolic process / response to oxidative stress / heme binding / metal ion binding
Similarity search - Function
Haem oxygenase conserved site / Heme oxygenase signature. / Haem oxygenase / Haem oxygenase-like / Heme oxygenase / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING CO / heme oxygenase (biliverdin-producing)
Similarity search - Component
Biological speciesCorynebacterium diphtheriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLabidi, R.J. / Faivre, B. / Carpentier, P. / Perard, J. / Gotico, P. / Li, Y. / Atta, M. / Fontecave, M.
Funding support France, 2items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-17-EURE-0003 France
Laboratories of Excellence (LabEx)ANR-11-LABX-0011 France
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Light-Activated Artificial CO 2 -Reductase: Structure and Activity.
Authors: Labidi, R.J. / Faivre, B. / Carpentier, P. / Perard, J. / Gotico, P. / Li, Y. / Atta, M. / Fontecave, M.
History
DepositionJun 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8393
Polymers24,1841
Non-polymers6552
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, MALLS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-28 kcal/mol
Surface area10270 Å2
Unit cell
Length a, b, c (Å)46.932, 55.111, 76.307
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein heme oxygenase (biliverdin-producing)


Mass: 24184.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium diphtheriae (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q54AI1, heme oxygenase (biliverdin-producing)
#2: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32CoN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: 20% PEG3350, 200 mM magnesium formate pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.87313 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 24, 2024
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.4→44.68 Å / Num. obs: 39800 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / CC1/2: 0.997 / Rrim(I) all: 0.187 / Net I/σ(I): 7.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.4 % / Num. unique obs: 1969 / CC1/2: 0.343 / Rrim(I) all: 3.01 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→44.68 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 1941 4.89 %
Rwork0.1746 --
obs0.1753 39701 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1669 0 44 302 2015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.563
X-RAY DIFFRACTIONf_dihedral_angle_d14.133704
X-RAY DIFFRACTIONf_chiral_restr0.065266
X-RAY DIFFRACTIONf_plane_restr0.007327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.30541490.31932569X-RAY DIFFRACTION97
1.43-1.470.27461180.27422691X-RAY DIFFRACTION100
1.47-1.520.2521360.25572663X-RAY DIFFRACTION100
1.52-1.570.26371290.23882667X-RAY DIFFRACTION100
1.57-1.620.25991450.23252687X-RAY DIFFRACTION100
1.62-1.690.24091310.21652659X-RAY DIFFRACTION100
1.69-1.760.2011100.19272696X-RAY DIFFRACTION100
1.76-1.860.2161370.18412685X-RAY DIFFRACTION100
1.86-1.970.19371400.17882696X-RAY DIFFRACTION100
1.97-2.120.16911200.16062719X-RAY DIFFRACTION100
2.12-2.340.16171480.15722701X-RAY DIFFRACTION100
2.34-2.680.20081560.15762709X-RAY DIFFRACTION100
2.68-3.370.15961540.15182747X-RAY DIFFRACTION100
3.37-44.680.16171680.14572871X-RAY DIFFRACTION100

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