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- PDB-1tk1: YEAST OXYGEN-DEPENDENT COPROPORPHYRINOGEN OXIDASE -

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Basic information

Entry
Database: PDB / ID: 1tk1
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 / cytoplasm / cytosol
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 - CHROMIUM SULFUR ANOMALOUS / Resolution: 1.9 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


Theoretical massNumber of molelcules
Total (without water)29,9361
Polymers29,9361
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.850, 70.850, 114.543
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-286-

HOH

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Components

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


Mass: 29935.641 Da / Num. of mol.: 1 / Fragment: truncated odCPO
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.: 92 / 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: 294 K / pH: 7.5
Details: 20% PEG 3000, 0.1 M HEPES, 0.2 M sodium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→59.76 Å / Num. obs: 21772 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 28.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 20
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 29.6 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 7 / Rsym value: 0.585 / % possible all: 95.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0001refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD - CHROMIUM SULFUR ANOMALOUS
Resolution: 1.9→59.76 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.86 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24907 1182 5.1 %RANDOM
Rwork0.21542 ---
obs0.21713 21772 96.86 %-
all-21772 --
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: 29.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refine analyzeLuzzati coordinate error free: 0.144 Å
Refinement stepCycle: LAST / Resolution: 1.9→59.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 0 92 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0211821
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9232462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0895219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09924.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69315305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3331511
X-RAY DIFFRACTIONr_chiral_restr0.1690.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021415
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2350.2875
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21242
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3950.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4311.51135
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.36121761
X-RAY DIFFRACTIONr_scbond_it3.2223799
X-RAY DIFFRACTIONr_scangle_it4.8794.5701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 75 -
Rwork0.222 1558 -
obs--95.16 %

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