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- PDB-2q71: Uroporphyrinogen Decarboxylase G168R single mutant enzyme in comp... -

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Basic information

Entry
Database: PDB / ID: 2q71
TitleUroporphyrinogen Decarboxylase G168R single mutant enzyme in complex with coproporphyrinogen-III
ComponentsUroporphyrinogen decarboxylase
KeywordsLYASE / Uroporphyrinogen Decarboxylase enzyme UROD G168R coproporphyrinogen-III product complex
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
COPROPORPHYRINOGEN III / Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 Uropophyrinogen 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 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 12, 2014Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5242
Polymers39,8631
Non-polymers6611
Water6,900383
1
A: Uroporphyrinogen decarboxylase
hetero molecules

A: Uroporphyrinogen decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,0474
Polymers79,7262
Non-polymers1,3222
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)103.037, 103.037, 71.865
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 asymmetric unit. The functional enzyme is a dimer of identical subunits. A crystallographic 2-fold generates teh biologically functional dimeric enzyme. The two identical active sites have been shown to act independently. One reaction product molecule (copropophyrinogen-III) is in the active site.

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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: Chemical ChemComp-CP3 / COPROPORPHYRINOGEN III


Mass: 660.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H44N4O8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protien 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) and equilibrated by sitting drop vapor diffusion against a well of ...Details: Protien 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) and equilibrated by sitting drop vapor diffusion against a well of precipitant., 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 19, 2003 / Details: Yale focusing mirrors
RadiationMonochromator: Yale Focusing mirrors, 1.5418 angstrom wavelength, 67 degrees of 0.5 degree oscillations (134 images, 0-67 degrees) plus 12 degrees of 0.25 degree oscillations (48 images 65-77 degrees)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 32683 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.078 / Χ2: 1.004 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.970.44228060.867182
1.97-2.050.3431350.914190.5
2.05-2.140.25432600.982194.3
2.14-2.250.20833461.011196.5
2.25-2.390.15933891.015197.5
2.39-2.580.1333861.057197.5
2.58-2.840.09733691.023196.8
2.84-3.250.06733761.073196
3.25-4.090.04633381.075194.5
4.09-300.04132780.961189.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ry3

1ry3


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.943 / SU ML: 0.087 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE CRYSTALS WERE ISOMORPHOUS TO 1RY3.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1135 3.5 %RANDOM
Rwork0.162 ---
obs0.164 32682 93.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.004 Å2
Baniso -1Baniso -2Baniso -3
1--1.51 Å2-0.76 Å20 Å2
2---1.51 Å20 Å2
3---2.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 48 383 3237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213144
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9624305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7365395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32122.752149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70115508
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0041531
X-RAY DIFFRACTIONr_chiral_restr0.0980.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022526
X-RAY DIFFRACTIONr_nbd_refined0.2030.21732
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22148
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.236
X-RAY DIFFRACTIONr_mcbond_it0.9041.51960
X-RAY DIFFRACTIONr_mcangle_it1.47623087
X-RAY DIFFRACTIONr_scbond_it2.24531343
X-RAY DIFFRACTIONr_scangle_it3.6254.51218
LS refinement shellResolution: 1.9→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 70 -
Rwork0.244 1957 -
obs-2027 80.15 %

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