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- PDB-9fw4: Crystal structure of Heme-Oxygenase mutant H20C from Corynebacter... -

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Basic information

Entry
Database: PDB / ID: 9fw4
TitleCrystal structure of Heme-Oxygenase mutant H20C from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))
Componentsheme oxygenase (biliverdin-producing)
KeywordsOXIDOREDUCTASE / carbon dioxyde photo-reduction 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: 2.3 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)
B: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5094
Polymers48,2702
Non-polymers1,2392
Water2,468137
1
A: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7552
Polymers24,1351
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7552
Polymers24,1351
Non-polymers6201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.744, 69.331, 63.177
Angle α, β, γ (deg.)90.00, 109.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein heme oxygenase (biliverdin-producing)


Mass: 24135.154 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG10000, 100 mM BIS-TRIS pH 5.5, 100 mM ammonium acetate

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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: 2.3→45.16 Å / Num. obs: 15723 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 34.5 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.093 / Rrim(I) all: 0.18 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1518 / CC1/2: 0.534 / Rpim(I) all: 0.62 / Rrim(I) all: 1.183 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.16 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2843 765 4.87 %
Rwork0.227 --
obs0.23 15702 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 86 137 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053534
X-RAY DIFFRACTIONf_angle_d1.3954811
X-RAY DIFFRACTIONf_dihedral_angle_d16.411321
X-RAY DIFFRACTIONf_chiral_restr0.035504
X-RAY DIFFRACTIONf_plane_restr0.003627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.34961500.29072953X-RAY DIFFRACTION98
2.48-2.730.36131500.28482975X-RAY DIFFRACTION98
2.73-3.120.3591620.26642968X-RAY DIFFRACTION99
3.12-3.930.27311180.21133028X-RAY DIFFRACTION99
3.93-45.160.23531850.19383013X-RAY DIFFRACTION99

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