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- PDB-2q6z: Uroporphyrinogen Decarboxylase G168R single mutant apo-enzyme -

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Basic information

Entry
Database: PDB / ID: 2q6z
TitleUroporphyrinogen Decarboxylase G168R single mutant apo-enzyme
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / Uroporphyrinogen Decarboxylase enzyme UROD G168R coproporphyrinogen
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 B biosynthetic process / heme A 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 B biosynthetic process / heme A 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPhillips, J.D. / Whitby, F.G. / Stadtmueller, B.M. / Edwards, C.Q. / Hill, C.P. / Kushner, J.P.
CitationJournal: Transl.Res. / Year: 2007
Title: Two novel uroporphyrinogen decarboxylase (URO-D) mutations causing hepatoerythropoietic porphyria (HEP).
Authors: Phillips, J.D. / Whitby, F.G. / Stadtmueller, B.M. / Edwards, C.Q. / Hill, C.P. / Kushner, J.P.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2007Provider: 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
Revision 1.4Oct 20, 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 1.5Aug 30, 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


Theoretical massNumber of molelcules
Total (without water)39,8631
Polymers39,8631
Non-polymers00
Water6,792377
1
A: Uroporphyrinogen decarboxylase

A: Uroporphyrinogen decarboxylase


Theoretical massNumber of molelcules
Total (without water)79,7262
Polymers79,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_676x-y+1,-y+2,-z+5/31
Unit cell
Length a, b, c (Å)103.236, 103.236, 72.398
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsThe crystal contains one monomer per asymmedtric unit. The functional enzyme is a dimer of identical subunits. A crystallographic 2-fold axis generates the biologically functional dimeric enzyme. The two identical active sites have been shown to act independently.

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Components

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


Mass: 39862.770 Da / Num. of mol.: 1 / Mutation: G168R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UROD / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3-pLysS / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.79 Å3/Da / Density % sol: 55.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at 6.5 mg/ml in 50mM Tris, pH 7.5, 1mM BME was mixed 5 parts to 3 parts of precipitant (1.7M citrate, pH 7.0), 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 II / Detector: IMAGE PLATE / Date: Sep 16, 2003 / Details: Yale focusing mirrors
RadiationMonochromator: Yale focusing mirrors, 1.5418 angstrom wavelength, 30 degrees of 0.5 degree oscillations (60 images 0-30 degrees) plus 45 independent degrees of 0.25 degree oscialltions (180 images 30 - 75 degrees).
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 30032 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.109 / Χ2: 1.102 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.497 / Num. unique all: 2974 / Χ2: 1.117 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URO

1uro


Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.233 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS CRYSTAL IS ISOMORPHOUS TO THAT IN 1URO
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1199 4 %RANDOM
Rwork0.174 ---
obs0.176 30010 98.63 %-
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: 30.153 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å2-1.18 Å20 Å2
2---2.36 Å20 Å2
3---3.53 Å2
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 0 0 377 3273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222979
X-RAY DIFFRACTIONr_bond_other_d0.0010.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9484063
X-RAY DIFFRACTIONr_angle_other_deg0.87436356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33922.979141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78315487
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5871528
X-RAY DIFFRACTIONr_chiral_restr0.0890.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02635
X-RAY DIFFRACTIONr_nbd_refined0.2280.2756
X-RAY DIFFRACTIONr_nbd_other0.1850.22978
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21442
X-RAY DIFFRACTIONr_nbtor_other0.0860.21741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.231
X-RAY DIFFRACTIONr_mcbond_it1.4031.52363
X-RAY DIFFRACTIONr_mcbond_other0.2011.5734
X-RAY DIFFRACTIONr_mcangle_it1.54122974
X-RAY DIFFRACTIONr_scbond_it2.23331314
X-RAY DIFFRACTIONr_scangle_it3.174.51089
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 105 -
Rwork0.24 2046 -
obs-2151 96.03 %

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