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- PDB-1r3r: Uroporphyrinogen Decarboxylase with mutation D86N -

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Basic information

Entry
Database: PDB / ID: 1r3r
TitleUroporphyrinogen Decarboxylase with mutation D86N
ComponentsUroporphyrinogen DecarboxylaseUroporphyrinogen III decarboxylase
KeywordsLYASE / uroporphyrinogen decarboxylase coproporphyrinogen / X-ray crystallography
Function / homology
Function and homology information


porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / porphyrin-containing compound metabolic process / protoporphyrinogen IX biosynthetic process / Heme biosynthesis / heme biosynthetic process ...porphyrin-containing compound catabolic process / uroporphyrinogen decarboxylase / uroporphyrinogen decarboxylase activity / heme B biosynthetic process / heme O biosynthetic process / heme A biosynthetic process / porphyrin-containing compound metabolic 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 / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsPhillips, J.D. / Whitby, F.G. / Kushner, J.P. / Hill, C.P.
CitationJournal: Embo J. / Year: 2003
Title: Structural basis for tetrapyrrole coordination by uroporphyrinogen decarboxylase
Authors: Phillips, J.D. / Whitby, F.G. / Kushner, J.P. / Hill, C.P.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 23, 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)40,8311
Polymers40,8311
Non-polymers00
Water6,864381
1
A: Uroporphyrinogen Decarboxylase

A: Uroporphyrinogen Decarboxylase


Theoretical massNumber of molelcules
Total (without water)81,6622
Polymers81,6622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
Unit cell
Length a, b, c (Å)102.735, 102.735, 73.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsOne URO-D monomer forms the asymmetric unit. URO-D is a dimer in solution and in the crystal. The dimer is formed by the 2-fold crystallographic rotation.

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Components

#1: Protein Uroporphyrinogen Decarboxylase / Uroporphyrinogen III decarboxylase / E.C.4.1.1.37 / URO-D / UPD


Mass: 40830.781 Da / Num. of mol.: 1 / Mutation: D86N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P06132, uroporphyrinogen decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.37 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 294 K / Method: liquid diffusion / pH: 6.5
Details: The crystal trial was conducted in an anaerobic chamber, with PBG, PBG-D added to the solution. These conditions are conducive to formation of an enzyme product complex, as the enzyme is ...Details: The crystal trial was conducted in an anaerobic chamber, with PBG, PBG-D added to the solution. These conditions are conducive to formation of an enzyme product complex, as the enzyme is typically active under these conditions (see related strcuture 1R3Q). There is not a ligand bound in this structure. 1.5 M citrate, pH 6.5, LIQUID DIFFUSION, temperature 294K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop / 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 RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→87.71 Å / Num. all: 36928 / Num. obs: 36928 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 9
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.437 / % possible all: 80
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 96 % / Num. measured all: 175858
Reflection shell
*PLUS
% possible obs: 79.8 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1URO

1uro


Resolution: 1.85→87.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.929 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19242 1122 3 %RANDOM
Rwork0.16117 ---
all0.16212 36928 --
obs0.16212 35762 95.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.283 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0.77 Å20 Å2
2---1.53 Å20 Å2
3---2.3 Å2
Refinement stepCycle: LAST / Resolution: 1.85→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 0 381 3370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0213082
X-RAY DIFFRACTIONr_bond_other_d0.0030.022817
X-RAY DIFFRACTIONr_angle_refined_deg1.691.9534212
X-RAY DIFFRACTIONr_angle_other_deg0.96136538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375393
X-RAY DIFFRACTIONr_chiral_restr0.1060.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023563
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02666
X-RAY DIFFRACTIONr_nbd_refined0.2310.2803
X-RAY DIFFRACTIONr_nbd_other0.250.23521
X-RAY DIFFRACTIONr_nbtor_other0.0870.21832
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2275
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.420.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3530.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.230
X-RAY DIFFRACTIONr_mcbond_it1.1191.51899
X-RAY DIFFRACTIONr_mcangle_it2.01923076
X-RAY DIFFRACTIONr_scbond_it3.09131183
X-RAY DIFFRACTIONr_scangle_it5.1774.51136
LS refinement shellResolution: 1.85→1.95 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.29 147
Rwork0.254 4365
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.161
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.69
LS refinement shell
*PLUS
Highest resolution: 1.85 Å / Lowest resolution: 1.95 Å / Rfactor Rfree: 0.29

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