- PDB-1txn: Crystal structure of coproporphyrinogen III oxidase -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1txn
Title
Crystal structure of coproporphyrinogen III oxidase
Components
Coproporphyrinogen III oxidase
Keywords
OXIDOREDUCTASE / 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 / 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
Resolution: 1.7→1.75 Å / Rmerge(I) obs: 0.379 / Num. unique all: 3677 / % possible all: 87.4
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Processing
Software
Name
Classification
CBASS
datacollection
HKL-2000
datareduction
SOLVE
phasing
SHARP
phasing
ARP/wARP
modelbuilding
CNS
refinement
HKL-2000
datascaling
Refinement
Method 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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.245
3714
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Random
Rwork
0.211
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all
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61016
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obs
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61016
93.4 %
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Displacement parameters
Biso mean: 34.5 Å2
Refinement step
Cycle: LAST / Resolution: 1.7→50 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4199
0
6
431
4636
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
c_bond_d
0.01
X-RAY DIFFRACTION
c_angle_deg
1.3
LS refinement shell
Resolution: 1.7→1.71 Å /
Rfactor
Num. reflection
Rfree
0.238
50
Rwork
0.238
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obs
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816
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