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- PDB-9mhr: G169L variant of Coproheme Decarboxylase from Streptomyces Coelic... -

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Basic information

Entry
Database: PDB / ID: 9mhr
TitleG169L variant of Coproheme Decarboxylase from Streptomyces Coelicolor 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
harderoheme (III) / Coproheme decarboxylase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCarriuolo, A.J. / 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

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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)144,45710
Polymers141,1455
Non-polymers3,3135
Water15,367853
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-19 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.253, 77.184, 77.361
Angle α, β, γ (deg.)114.44, 98.16, 110.50
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28228.900 Da / Num. of mol.: 5 / Mutation: G169L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: chdC, SCO6042 / Production host: Escherichia coli BL21(DE3) (bacteria)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / 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: 2.28 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 12% PEG 3350, 100 mM sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 8, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 210513 / % possible obs: 95 % / Redundancy: 3.4 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.039 / Rrim(I) all: 0.072 / Χ2: 1.545 / Net I/σ(I): 12.2 / Num. measured all: 712116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.53.30.347199800.8960.9720.2230.4140.43490.3
1.5-1.563.60.266209590.950.9870.1620.3120.50194.3
1.56-1.633.60.198209710.9660.9910.1210.2330.56294.8
1.63-1.723.50.148211610.9760.9940.0920.1750.67295.3
1.72-1.833.40.11211570.9850.9960.0690.130.88495.6
1.83-1.9730.082212360.9850.9960.0580.1021.4195.9
1.97-2.173.40.068212570.9920.9980.0440.0822.04795.8
2.17-2.483.50.059214540.9910.9980.0370.072.55996.9
2.48-3.123.30.051213170.9950.9990.0330.0613.11296.3
1.45-1.53.20.043210210.9950.9990.0290.0523.54894.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→41.1 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 18.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1819 1989 1.04 %
Rwork0.1665 --
obs0.1666 191016 95.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8974 0 230 853 10057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d9.4531521
X-RAY DIFFRACTIONf_chiral_restr0.0571320
X-RAY DIFFRACTIONf_plane_restr0.0111652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.23281420.198413324X-RAY DIFFRACTION94
1.74-1.810.191440.172713516X-RAY DIFFRACTION96
1.81-1.890.2211460.172313572X-RAY DIFFRACTION96
1.89-1.990.20071370.176913591X-RAY DIFFRACTION96
1.99-2.110.17991410.173613458X-RAY DIFFRACTION95
2.11-2.280.20631470.171813709X-RAY DIFFRACTION97
2.28-2.510.19911450.174413697X-RAY DIFFRACTION97
2.51-2.870.17391400.170913700X-RAY DIFFRACTION97

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