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- PDB-2aex: The 1.58A Crystal Structure of Human Coproporphyrinogen Oxidase R... -

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Basic information

Entry
Database: PDB / ID: 2aex
TitleThe 1.58A Crystal Structure of Human Coproporphyrinogen Oxidase Reveals the Structural Basis of Hereditary Coproporphyria
ComponentsCoproporphyrinogen III oxidase, mitochondrial
KeywordsOXIDOREDUCTASE / flat beta-sheet sandwiched by helices
Function / homology
Function and homology information


coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / structural constituent of eye lens / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / mitochondrial intermembrane space ...coproporphyrinogen oxidase / coproporphyrinogen oxidase activity / heme O biosynthetic process / heme B biosynthetic process / heme A biosynthetic process / structural constituent of eye lens / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process / mitochondrial intermembrane space / protein homodimerization activity / mitochondrion / membrane / 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
CITRIC ACID / Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsLee, D.S. / Flachsova, E. / Bodnarova, M. / Demeler, B. / Martasek, P. / Raman, C.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structural basis of hereditary coproporphyria.
Authors: Lee, D.S. / Flachsova, E. / Bodnarova, M. / Demeler, B. / Martasek, P. / Raman, C.S.
History
DepositionJul 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6432
Polymers39,4511
Non-polymers1921
Water6,539363
1
A: Coproporphyrinogen III oxidase, mitochondrial
hetero molecules

A: Coproporphyrinogen III oxidase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2864
Polymers78,9012
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)112.741, 112.741, 112.741
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-710-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -X, -Y+1, Z

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Components

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


Mass: 39450.664 Da / Num. of mol.: 1 / Fragment: coproporphyrinogen oxidase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPOX, CPO, CPX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36551, coproporphyrinogen oxidase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MPD, citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9537 0.9795 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2003
RadiationMonochromator: mirrors / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97951
30.97961
ReflectionResolution: 1.5→100 Å / Num. all: 65081 / Num. obs: 65081 / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 1.58→1.62 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→31.31 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.014 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20755 3294 5.1 %RANDOM
Rwork0.18598 ---
obs0.18709 61787 99.47 %-
all-65081 --
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: 28.411 Å2
Refinement stepCycle: LAST / Resolution: 1.58→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 13 363 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212920
X-RAY DIFFRACTIONr_bond_other_d0.0050.022560
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.953966
X-RAY DIFFRACTIONr_angle_other_deg0.76835983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9685365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94323.311148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64615500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6361526
X-RAY DIFFRACTIONr_chiral_restr0.0780.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023366
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02641
X-RAY DIFFRACTIONr_nbd_refined0.2080.2663
X-RAY DIFFRACTIONr_nbd_other0.1990.22622
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21436
X-RAY DIFFRACTIONr_nbtor_other0.0860.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2297
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1152.52283
X-RAY DIFFRACTIONr_mcbond_other0.3442.5713
X-RAY DIFFRACTIONr_mcangle_it2.2683.52853
X-RAY DIFFRACTIONr_scbond_it2.0232.51353
X-RAY DIFFRACTIONr_scangle_it2.563.51113
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 246 -
Rwork0.23 4479 -
obs--99.52 %
Refinement TLS params.Method: refined / Origin x: 21.207 Å / Origin y: 55.4269 Å / Origin z: 27.1905 Å
111213212223313233
T-0.0304 Å2-0.0009 Å2-0.0195 Å2--0.0119 Å20.0209 Å2---0.0297 Å2
L0.7865 °20.1379 °2-0.3414 °2-0.7724 °20.1345 °2--0.5557 °2
S-0.0334 Å °0.054 Å °-0.047 Å °-0.0515 Å °-0.017 Å °-0.0347 Å °0.0607 Å °0.0036 Å °0.0504 Å °

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