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- PDB-1txn: Crystal structure of coproporphyrinogen III oxidase -

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Basic information

Entry
Database: PDB / ID: 1txn
TitleCrystal structure of coproporphyrinogen III oxidase
ComponentsCoproporphyrinogen III oxidase
KeywordsOXIDOREDUCTASE / Structural genomics / Dimer / Novel fold / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / Heme biosynthesis / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, aerobic / Coproporphyrinogen III oxidase, conserved site / Oxygen-dependent coproporphyrinogen III oxidase superfamily / Coproporphyrinogen III oxidase / Coproporphyrinogen III oxidase signature. / oxygen-dependent coproporphyrinogen oxidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxygen-dependent coproporphyrinogen-III oxidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of coproporphyrinogen III oxidase
Authors: Kumaran, D. / Swaminathan, S.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coproporphyrinogen III oxidase
B: Coproporphyrinogen III oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3693
Polymers76,2772
Non-polymers921
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-28 kcal/mol
Surface area22040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.754, 71.754, 117.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Coproporphyrinogen III oxidase / / Coproporphyrinogenase / Coprogen oxidase / COX


Mass: 38138.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HEM13, YDR044W, YD5112.02 / Production host: Escherichia coli (E. coli) / References: UniProt: P11353, coproporphyrinogen oxidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 8000, Sodium Cacodylate, Magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 6, 2003 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 61551 / Num. obs: 61551 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.2 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.5
Reflection shellResolution: 1.7→1.75 Å / Rmerge(I) obs: 0.379 / Num. unique all: 3677 / % possible all: 87.4

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Processing

Software
NameClassification
CBASSdata collection
HKL-2000data reduction
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 97-106 and 271-328 in chain A, and residues 97-106, 203-205, and 271-328 in chain B, were not visbile in the electron density and hence not modeled
RfactorNum. reflection% reflectionSelection details
Rfree0.245 3714 -Random
Rwork0.211 ---
all-61016 --
obs-61016 93.4 %-
Displacement parametersBiso mean: 34.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4199 0 6 431 4636
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.7→1.71 Å /
RfactorNum. reflection
Rfree0.238 50
Rwork0.238 -
obs-816

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