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- PDB-3gvq: UROD single-chain dimer -

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Basic information

Entry
Database: PDB / ID: 3gvq
TitleUROD single-chain dimer
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / heme / uroporphyrinogen / DECARBOXYLASE / ALPHA-8-BETA-8 BARREL / Acetylation / Cytoplasm / Disease mutation / Heme biosynthesis / Phosphoprotein / Porphyrin biosynthesis
Function / homology
Function and homology information


porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme A biosynthetic process / heme B biosynthetic process / : / Heme biosynthesis / heme biosynthetic process / nucleoplasm / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2.1 Å
AuthorsHill, C.P. / Phillips, J.D. / Warby, C. / Whitby, F.G. / Kushner, J.P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Substrate shuttling between active sites of uroporphyrinogen decarboxylase is not required to generate coproporphyrinogen.
Authors: Phillips, J.D. / Warby, C.A. / Whitby, F.G. / Kushner, J.P. / Hill, C.P.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)40,8321
Polymers40,8321
Non-polymers00
Water2,612145
1
A: Uroporphyrinogen decarboxylase

A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,6642
Polymers81,6642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area2450 Å2
ΔGint-10 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.145, 103.145, 71.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-443-

HOH

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Components

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


Mass: 40831.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / Plasmid: 511693 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.68 Å3/Da / Density % sol: 54.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: CITRATE BUFFER, PH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 11, 2003
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 25394 / Num. obs: 25394 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 9.9
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2197 / Rsym value: 0.4 / % possible all: 86.3

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: molecular replacement
Starting model: PDB entry 1uro

1uro


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.827 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24411 1298 5.1 %RANDOM
Rwork0.19261 ---
all0.19517 24075 --
obs0.19517 24075 97.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.231 Å2
Baniso -1Baniso -2Baniso -3
1--2.17 Å2-1.09 Å20 Å2
2---2.17 Å20 Å2
3---3.26 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 145 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222879
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9523915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65223.233133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56915467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0541524
X-RAY DIFFRACTIONr_chiral_restr0.0870.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022235
X-RAY DIFFRACTIONr_nbd_refined0.2060.21478
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21969
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.214
X-RAY DIFFRACTIONr_mcbond_it0.9081.51841
X-RAY DIFFRACTIONr_mcangle_it1.53622870
X-RAY DIFFRACTIONr_scbond_it2.03231186
X-RAY DIFFRACTIONr_scangle_it3.2734.51045
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 82 -
Rwork0.231 1558 -
obs--85.77 %

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