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- PDB-2inf: Crystal Structure of Uroporphyrinogen Decarboxylase from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 2inf
TitleCrystal Structure of Uroporphyrinogen Decarboxylase from Bacillus subtilis
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / (alpha-beta)8 barrel / eight parallel beta strands surrounded by eight alpha helices
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
Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFan, J. / Liu, Q. / Hao, Q. / Teng, M.K. / Niu, L.W.
CitationJournal: J.Bacteriol. / Year: 2007
Title: Crystal structure of uroporphyrinogen decarboxylase from Bacillus subtilis
Authors: Fan, J. / Liu, Q. / Hao, Q. / Teng, M.K. / Niu, L.W.
History
DepositionOct 6, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase
B: Uroporphyrinogen decarboxylase
C: Uroporphyrinogen decarboxylase
D: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)162,0264
Polymers162,0264
Non-polymers00
Water4,612256
1
A: Uroporphyrinogen decarboxylase
B: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,0132
Polymers81,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uroporphyrinogen decarboxylase
D: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,0132
Polymers81,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.612, 80.410, 90.940
Angle α, β, γ (deg.)68.68, 89.64, 80.82
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 40506.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P32395, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 2000, 100mM citrate, 160mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 67725 / Num. obs: 65152 / % possible obs: 96.2 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Rsym value: 0.063
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 2.4 % / Rsym value: 0.406 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
AUTOMARdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1URO

1uro


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 16.099 / SU ML: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.37 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25125 3316 5.1 %RANDOM
Rwork0.19744 ---
all0.205 64278 --
obs0.20013 61835 96.23 %-
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: 53.559 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20.11 Å2-0.29 Å2
2---0.85 Å21.36 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10772 0 0 256 11028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02211040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.291.97314976
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92151372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33725.042476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.357151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0151540
X-RAY DIFFRACTIONr_chiral_restr0.0920.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028356
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.25370
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.27545
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2477
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5151.57077
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.875211036
X-RAY DIFFRACTIONr_scbond_it1.27234598
X-RAY DIFFRACTIONr_scangle_it2.0034.53940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 238 -
Rwork0.265 4483 -
obs--94.36 %

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