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- PDB-2eja: Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex ... -

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Basic information

Entry
Database: PDB / ID: 2eja
TitleCrystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / Uroporphyrinogen Decarboxylase / Dimer / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / cytosol
Similarity search - Function
Uroporphyrinogen decarboxylase HemE / Uroporphyrinogen decarboxylase signature 1. / Uroporphyrinogen decarboxylase signature 2. / Uroporphyrinogen decarboxylase (URO-D) / Uroporphyrinogen decarboxylase (URO-D) / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex aeolicus
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionMar 16, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uroporphyrinogen decarboxylase
B: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5193
Polymers77,4592
Non-polymers591
Water13,529751
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-9.1 kcal/mol
Surface area25290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.473, 80.403, 128.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uroporphyrinogen decarboxylase / URO-D / UPD


Mass: 38729.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)RIL / References: UniProt: O66667, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 751 / 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: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 4.5
Details: 50v/v(%) PEG 200, 0.1M Acetic acid, pH 4.5, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 10, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→26.8 Å / Num. all: 54412 / Num. obs: 50375 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.049 / Net I/σ(I): 21.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 8.1 / Num. unique all: 3400 / Rsym value: 0.238 / % possible all: 63.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2INF

2inf


Resolution: 1.9→26.79 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2512 -RANDOM
Rwork0.205 ---
obs0.205 50375 92.6 %-
all-54412 --
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å20 Å2
2--1.62 Å20 Å2
3---1.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.02 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5451 0 4 751 6206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.27 163 -
Rwork0.204 --
obs-3400 63.1 %

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