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- PDB-1uro: UROPORPHYRINOGEN DECARBOXYLASE -

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Basic information

Entry
Database: PDB / ID: 1uro
TitleUROPORPHYRINOGEN DECARBOXYLASE
ComponentsPROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)
KeywordsLYASE / DECARBOXYLASE / ALPHA-8-BETA-8 BARREL / HEME BIOSYNTHESIS / PORPHYRIN / UROPORPHYRINOGEN
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
BETA-MERCAPTOETHANOL / Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWhitby, F.G. / Phillips, J.D. / Kushner, J.P. / Hill, C.P.
CitationJournal: 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 21, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 26, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9102
Polymers40,8321
Non-polymers781
Water5,080282
1
A: PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)
hetero molecules

A: PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,8204
Polymers81,6642
Non-polymers1562
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)103.000, 103.000, 73.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PROTEIN (UROPORPHYRINOGEN DECARBOXYLASE) / URO-D / UROD


Mass: 40831.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: HIS-TAG CLEAVED / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 55.47 %
Crystal growpH: 6 / Details: CITRATE BUFFER, pH 6.0
Crystal
*PLUS
Density % sol: 54 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
236 mMTris-HCl1droppH7.5
30.7 mMbeta-mercaptoethanol1drop
47 %glycerol1drop
50.3-0.5 Mcitrate1drop
61.2-1.7 Mcitrate1reservoirpH5.8-6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9252, 0.9795, 0.9798, 1.0688
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 6, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92521
20.97951
30.97981
41.06881
ReflectionResolution: 1.8→20 Å / Num. obs: 42721 / % possible obs: 96.2 % / Observed criterion σ(I): -2 / Redundancy: 4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.5 / Rsym value: 0.176 / % possible all: 91.7
Reflection
*PLUS
Num. measured all: 156721
Reflection shell
*PLUS
% possible obs: 91.7 %

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Processing

Software
NameVersionClassification
XTALVIEWrefinement
PHASESphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1067 2.5 %RANDOM
Rwork0.184 ---
obs0.184 41570 97 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 4 282 3088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.049
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3077 126 2.5 %
Rwork0.2835 4913 -
obs--97.1 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 2.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
% reflection Rfree: 2.5 %

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