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

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Basic information

Entry
Database: PDB / ID: 3gvr
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: 2.2 Å
AuthorsHill, C.P. / Phillips, J.D. / Whitby, F.G. / Warby, C.
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 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)40,8321
Polymers40,8321
Non-polymers00
Water2,252125
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 area2430 Å2
ΔGint-11 kcal/mol
Surface area26480 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.447, 103.447, 70.716
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: 40831.766 Da / Num. of mol.: 1
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.: 125 / 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: 54.02 %
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
ReflectionAv σ(I) over netI: 15.35 / Number: 135250 / Rmerge(I) obs: 0.11 / Χ2: 1.03 / D res high: 2.2 Å / D res low: 40 Å / Num. obs: 22288 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
4.744096.110.0691.285
3.764.749910.0861.39
3.293.7699.810.1031.086
2.993.2999.810.1381.078
2.772.9910010.1760.937
2.612.7799.910.2270.952
2.482.6199.910.2730.858
2.372.4810010.310.81
2.282.3799.910.3730.842
2.22.2898.610.3950.862
ReflectionResolution: 2.2→40 Å / Num. obs: 22288 / % possible obs: 99.3 % / Rmerge(I) obs: 0.11 / Χ2: 1.029 / Net I/σ(I): 15.353
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.280.39521860.86298.6
2.28-2.370.37322070.84299.9
2.37-2.480.3122030.81100
2.48-2.610.27322360.85899.9
2.61-2.770.22722090.95299.9
2.77-2.990.17622330.937100
2.99-3.290.13822321.07899.8
3.29-3.760.10322481.08699.8
3.76-4.740.08622621.3999
4.74-400.06922721.28596.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementResolution: 2.2→14.73 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.822 / SU B: 6.084 / SU ML: 0.155 / SU R Cruickshank DPI: 0.243 / SU Rfree: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH Y164 MUTATED TO A G IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN IS A SINGLE-CHAIN FUSION DIMER OF HUMAN UROD WITH Y164 MUTATED TO A G IN THE FIRST OF THE TWO HALVES. BECAUSE THE CRYSTAL IS ISOMORPHOUS WITH WTUROD IN WHICH THERE IS A MONOMER IN THE ASYMMETRIC UNIT, THE AUTHORS HAVE MODELED Y164 AT ONE-HALF OCCUPANCY. THIS ACCOUNTS FOR THE STOCHASTIC ARRANGEMENT OF THE FUSION DIMER IN THE CRYSTAL SUCH THAT RESIDUE 164 IS EFFECTIVELY HALF Y AND HALF G.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1145 5.1 %RANDOM
Rwork0.194 ---
obs0.197 22265 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.03 Å2 / Biso mean: 39.999 Å2 / Biso min: 19.13 Å2
Baniso -1Baniso -2Baniso -3
1--2.06 Å2-1.03 Å20 Å2
2---2.06 Å20 Å2
3---3.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→14.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 0 125 2930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222879
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9523915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.823.233133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96315467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3511524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022235
X-RAY DIFFRACTIONr_nbd_refined0.2090.21365
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.211
X-RAY DIFFRACTIONr_mcbond_it0.8611.51837
X-RAY DIFFRACTIONr_mcangle_it1.50422870
X-RAY DIFFRACTIONr_scbond_it1.92931184
X-RAY DIFFRACTIONr_scangle_it3.1384.51045
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 70 -
Rwork0.234 1474 -
all-1544 -
obs--95.84 %

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