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- PDB-3gvv: Single-chain UROD Y164G (GY) mutation -

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Basic information

Entry
Database: PDB / ID: 3gvv
TitleSingle-chain UROD Y164G (GY) mutation
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / uroporphyrinogen / decarboxylase / heme biosynthesis / Acetylation / Cytoplasm / Disease mutation / 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 O biosynthetic process / heme A biosynthetic process / heme B biosynthetic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme O biosynthetic process / heme A biosynthetic process / heme B biosynthetic process / protoporphyrinogen IX 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 / Resolution: 2.8 Å
AuthorsHill, C.P. / Phillips, J.D. / Whitby, F.G. / Warby, C. / 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 13, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)40,8481
Polymers40,8481
Non-polymers00
Water45025
1
A: Uroporphyrinogen decarboxylase

A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,6962
Polymers81,6962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Buried area2380 Å2
ΔGint-10 kcal/mol
Surface area26270 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.931, 102.931, 72.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 40847.766 Da / Num. of mol.: 1 / Mutation: F217Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / 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.: 25 / 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: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growMethod: hanging drop / Details: hanging drop

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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: Aug 18, 2008 / Details: yale mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 12 % / Av σ(I) over netI: 13.74 / Number: 131959 / Rmerge(I) obs: 0.183 / Χ2: 1.04 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 10977 / % possible obs: 98.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.034010010.1821.45714.5
4.796.0310010.1290.99514.9
4.184.7910010.130.98515.2
3.84.1810010.1621.04115.2
3.533.810010.2160.9914.5
3.323.5310010.2750.9913.2
3.153.3299.910.3350.93711.2
3.023.1598.910.380.9038.8
2.93.0295.510.4430.8576.2
2.82.985.910.4550.9174.6
ReflectionResolution: 2.8→40 Å / Num. obs: 10977 / % possible obs: 98.1 % / Redundancy: 12 % / Rmerge(I) obs: 0.183 / Χ2: 1.04 / Net I/σ(I): 13.742
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.94.60.4559330.91785.9
2.9-3.026.20.44310610.85795.5
3.02-3.158.80.3810790.90398.9
3.15-3.3211.20.33511250.93799.9
3.32-3.5313.20.27510830.99100
3.53-3.814.50.21611280.99100
3.8-4.1815.20.16211081.041100
4.18-4.7915.20.1311330.985100
4.79-6.0314.90.12911330.995100
6.03-4014.50.18211941.457100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.8→33.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.166 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.82 / SU B: 14.486 / SU ML: 0.282 / SU Rfree: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE FIRST OF THE TWO ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH F217 MUTATED TO A Y IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, WE HAVE MODELED Y217 IN TWO CONFORMATIONS AT ONE-HALF OCCUPANCY EACH. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 217 IS EFFECTIVELY HALF F AND HALF Y.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1067 9.7 %RANDOM
Rwork0.172 ---
obs0.181 10954 97.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 104.68 Å2 / Biso mean: 50.378 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.74 Å2-1.37 Å20 Å2
2---2.74 Å20 Å2
3---4.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2811 0 0 25 2836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222884
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.973921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57323.209134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.51915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3371524
X-RAY DIFFRACTIONr_chiral_restr0.1090.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212239
X-RAY DIFFRACTIONr_mcbond_it0.8021.51784
X-RAY DIFFRACTIONr_mcangle_it1.622867
X-RAY DIFFRACTIONr_scbond_it2.25831100
X-RAY DIFFRACTIONr_scangle_it4.0284.51054
LS refinement shellResolution: 2.8→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 58 -
Rwork0.241 607 -
all-665 -
obs--82.61 %

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