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- PDB-1tkl: Yeast Oxygen-Dependent Coproporphyrinogen Oxidase -

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Basic information

Entry
Database: PDB / ID: 1tkl
TitleYeast Oxygen-Dependent Coproporphyrinogen Oxidase
ComponentsCoproporphyrinogen III oxidase
KeywordsOXIDOREDUCTASE / coproporphyrinogen oxidase / heme biosynthesis / enzyme
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 / Chromium sulfur SAD / Resolution: 2 Å
AuthorsPhillips, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of the Oxygen-dependant Coproporphyrinogen Oxidase (Hem13p) of Saccharomyces cerevisiae
Authors: Phillips, J.D. / Whitby, F.G. / Warby, C.A. / Labbe, P. / Yang, C. / Pflugrath, J.W. / Ferrara, J.D. / Robinson, H. / Kushner, J.P. / Hill, C.P.
History
DepositionJun 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)75,0702
Polymers75,0702
Non-polymers00
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-11 kcal/mol
Surface area28730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.822, 86.822, 207.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 37535.230 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 / Plasmid: pET16B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)plysS / References: UniProt: P11353, coproporphyrinogen oxidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.3 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG 8000, 0.1 M HEPES, 2% isopropanol, 0.2 M sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 51064 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 19
Reflection shellResolution: 2→2.07 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5248 / Rsym value: 0.583 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: Chromium sulfur SAD / Resolution: 2→79.06 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.636 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25828 2732 5.1 %RANDOM
Rwork0.20757 ---
all0.2101 51064 --
obs0.2101 51064 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--1.5 Å20 Å2
3----2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.173 Å0.184 Å
Refinement stepCycle: LAST / Resolution: 2→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5291 0 0 418 5709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215190
X-RAY DIFFRACTIONr_bond_other_d0.0010.024514
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9197032
X-RAY DIFFRACTIONr_angle_other_deg0.898310520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.295616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3423.433268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04315860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9441539
X-RAY DIFFRACTIONr_chiral_restr0.0990.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021129
X-RAY DIFFRACTIONr_nbd_refined0.2110.21134
X-RAY DIFFRACTIONr_nbd_other0.1970.24658
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22462
X-RAY DIFFRACTIONr_nbtor_other0.0880.22904
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2423
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.210
X-RAY DIFFRACTIONr_mcbond_it1.5081.53951
X-RAY DIFFRACTIONr_mcbond_other0.2381.51256
X-RAY DIFFRACTIONr_mcangle_it1.69624965
X-RAY DIFFRACTIONr_scbond_it2.24232540
X-RAY DIFFRACTIONr_scangle_it3.074.52066
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 186 -
Rwork0.254 3676 -
obs--97.4 %

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