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- PDB-1jpk: Gly156Asp mutant of Human UroD, human uroporphyrinogen III decarb... -

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Basic information

Entry
Database: PDB / ID: 1jpk
TitleGly156Asp mutant of Human UroD, human uroporphyrinogen III decarboxylase
ComponentsUROPORPHYRINOGEN DECARBOXYLASEUroporphyrinogen III decarboxylase
KeywordsLYASE / heme biosynthesis
Function / homology
Function and homology information


porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / porphyrin-containing compound metabolic process / heme B biosynthetic process / heme O 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 B biosynthetic process / heme O 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: 2.2 Å
AuthorsPhillips, J.D. / Parker, T.L. / Schubert, H.L. / Whitby, F.G. / Hill, C.P. / Kushner, J.P.
Citation
Journal: Blood / Year: 2001
Title: Functional consequences of naturally occurring mutations in human uroporphyrinogen decarboxylase.
Authors: Phillips, J.D. / Parker, T.L. / Schubert, H.L. / Whitby, F.G. / Hill, C.P. / Kushner, J.P.
#1: Journal: Embo J. / Year: 1998
Title: Crystal Structure of Human Uroporphyrinogen Decarboxylase
Authors: Whitby, F.G. / Phillips, J.D. / Kushner, J.P. / Hill, C.P.
History
DepositionAug 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 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)43,4241
Polymers43,4241
Non-polymers00
Water4,720262
1
A: UROPORPHYRINOGEN DECARBOXYLASE

A: UROPORPHYRINOGEN DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)86,8472
Polymers86,8472
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)103.2, 103.2, 73.62
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
Detailsphysiological dimer, monomer in the ASU

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Components

#1: Protein UROPORPHYRINOGEN DECARBOXYLASE / Uroporphyrinogen III decarboxylase / UroD / UPD / uro'gen III decarboxylase


Mass: 43423.531 Da / Num. of mol.: 1 / Mutation: G156D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UroD / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon + / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.6 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD and MES, or CITRATE, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Details: Phillips, J.D., (1997) Protein Sci., 6, 1343.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
250 mMTris1droppH7.5
310 %glycerol1drop
41 mMbeta-mercaptoethanol1drop
516 %MPD1reservoir
60.1 MES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 22708 / Num. obs: 22708 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.84
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.39 / % possible all: 99.2
Reflection
*PLUS
Num. obs: 23423 / Num. measured all: 274282
Reflection shell
*PLUS
% possible obs: 99.2 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1URO

1uro


Resolution: 2.2→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1100 5 %5%
Rwork0.195 ---
all-22198 --
obs-22198 97.1 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2806 0 0 262 3068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_bond_d0.13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.30.30581500.2819X-RAY DIFFRACTION2623
2.3-2.420.32081520.2636X-RAY DIFFRACTION2594
2.42-2.570.32211280.2467X-RAY DIFFRACTION2663
3.05-3.490.22341210.1861X-RAY DIFFRACTION2669
3.49-4.40.16951330.1416X-RAY DIFFRACTION2665
4.4-1000.20651330.1702X-RAY DIFFRACTION2613
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.13
X-RAY DIFFRACTIONx_angle_deg2.4
LS refinement shell
*PLUS
Lowest resolution: 2.3 Å

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