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- PDB-9fy4: Crystal structure of Heme-Oxygenase mutant I143K from Corynebacte... -

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Basic information

Entry
Database: PDB / ID: 9fy4
TitleCrystal structure of Heme-Oxygenase mutant I143K from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))
Componentsheme oxygenase (biliverdin-producing)
KeywordsOXIDOREDUCTASE / carbon dioxide 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: 2.839 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
DepositionJul 2, 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)
H: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7066
Polymers48,3722
Non-polymers1,3344
Water2,252125
1
A: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8653
Polymers24,1861
Non-polymers6792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: heme oxygenase (biliverdin-producing)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8413
Polymers24,1861
Non-polymers6552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.681, 63.525, 76.120
Angle α, β, γ (deg.)90.00, 97.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein heme oxygenase (biliverdin-producing)


Mass: 24186.180 Da / Num. of mol.: 2 / Mutation: I143K
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-COH / PROTOPORPHYRIN IX CONTAINING CO


Mass: 619.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32CoN4O4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 25% PEG3350, 100 mM BIS-TRIS pH 5.5, 200 mM NaCl

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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 14, 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: 2.839→48.61 Å / Num. obs: 9301 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 0.961 / Rpim(I) all: 0.172 / Rrim(I) all: 0.307 / Net I/σ(I): 3.8
Reflection shellResolution: 2.839→2.99 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1291 / CC1/2: 0.673 / Rpim(I) all: 0.575 / Rrim(I) all: 1.035 / % possible all: 94.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.839→48.61 Å / Cor.coef. Fo:Fc: 0.809 / Cor.coef. Fo:Fc free: 0.781 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.528
RfactorNum. reflection% reflectionSelection details
Rfree0.3061 428 4.61 %RANDOM
Rwork0.234 ---
obs0.2372 9291 98.3 %-
Displacement parametersBiso mean: 44.21 Å2
Baniso -1Baniso -2Baniso -3
1--37.6125 Å20 Å210.2137 Å2
2--6.6603 Å20 Å2
3---30.9522 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.839→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 88 125 3529
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0053483HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.894730HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1244SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes608HARMONIC5
X-RAY DIFFRACTIONt_it3483HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.81
X-RAY DIFFRACTIONt_other_torsion18.2
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion408SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2693SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.9 Å / Total num. of bins used: 22
RfactorNum. reflection% reflection
Rfree0.3236 -4.51 %
Rwork0.3171 423 -
all0.3174 443 -
obs--84.53 %

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