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- PDB-9mhq: G169V variant of Streptomyces coelicolor coproheme decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 9mhq
TitleG169V variant of Streptomyces coelicolor coproheme decarboxylase in complex with Monovinyl, Monopropionate Deuteroheme
ComponentsCoproheme decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / heme biosynthesis / oxidative decarboxylase
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor / hydrogen peroxide-dependent heme synthase / heme B biosynthetic process / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PHOSPHATE ION / harderoheme (III) / Coproheme decarboxylase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsCarriuolo, A.C. / Lanzilotta, W.N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Role of Conserved Elements in an Active Site a-Helix of Coproheme Decarboxylase
Authors: Carriuolo, A.J. / Lanzilotta, W.N.
History
DepositionDec 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coproheme decarboxylase
B: Coproheme decarboxylase
C: Coproheme decarboxylase
D: Coproheme decarboxylase
E: Coproheme decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,79015
Polymers141,0745
Non-polymers3,71510
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17250 Å2
ΔGint-65 kcal/mol
Surface area38780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.747, 132.747, 122.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
Coproheme decarboxylase / Coproheme III oxidative decarboxylase / Hydrogen peroxide-dependent heme synthase


Mass: 28214.873 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: chdC, SCO6042 / Production host: Escherichia coli (E. coli)
References: UniProt: O69830, hydrogen peroxide-dependent heme synthase
#2: Chemical
ChemComp-VOV / harderoheme (III)


Mass: 662.513 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C35H34FeN4O6
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 291 K / Method: batch mode
Details: Protein (500 uM) prepared with coproheme (15 mg/mL) in 100 mM HEPES/100 mM KCl pH7.5 buffer and 10 mM of KCN. Batch crystallization against a solution of 0.2 ammonium phosphate pH 7.0, 20% ...Details: Protein (500 uM) prepared with coproheme (15 mg/mL) in 100 mM HEPES/100 mM KCl pH7.5 buffer and 10 mM of KCN. Batch crystallization against a solution of 0.2 ammonium phosphate pH 7.0, 20% w/v polyethylene glycol 3,350, and 200mM betaine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Feb 15, 2023
RadiationMonochromator: 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 86577 / % possible obs: 97.9 % / Redundancy: 8.9 % / CC1/2: 0.99 / CC star: 0.997 / Net I/σ(I): 13.7
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 8617 / CC1/2: 0.564 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→43.45 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2002 2.37 %
Rwork0.1898 --
obs0.1905 84601 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9142 0 251 201 9594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d8.6391531
X-RAY DIFFRACTIONf_chiral_restr0.0671338
X-RAY DIFFRACTIONf_plane_restr0.0091681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.31561460.2615946X-RAY DIFFRACTION99
2.02-2.070.27881470.24516002X-RAY DIFFRACTION100
2.07-2.130.26871420.23445975X-RAY DIFFRACTION100
2.13-2.20.24041470.2266036X-RAY DIFFRACTION100
2.2-2.280.2531450.20986008X-RAY DIFFRACTION100
2.28-2.370.26061450.2176031X-RAY DIFFRACTION100
2.37-2.480.28321420.21425987X-RAY DIFFRACTION100
2.48-2.610.25741480.21926040X-RAY DIFFRACTION100
2.61-2.770.25081450.20636028X-RAY DIFFRACTION100
2.77-2.990.2561490.20526016X-RAY DIFFRACTION100
2.99-3.290.21741400.18146063X-RAY DIFFRACTION100
3.29-3.760.1621310.16495467X-RAY DIFFRACTION90
3.76-4.740.1791210.1554898X-RAY DIFFRACTION81
4.74-43.450.1771540.17296102X-RAY DIFFRACTION100

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