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- PDB-1r3t: Uroporphyrinogen Decarboxylase single mutant D86G in complex with... -

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Basic information

Entry
Database: PDB / ID: 1r3t
TitleUroporphyrinogen Decarboxylase single mutant D86G in complex with coproporphyrinogen-III
ComponentsUroporphyrinogen Decarboxylase
KeywordsLYASE / uroporphyrinogen decarboxylase coproporphyrinogen / X-ray crystallography
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 A biosynthetic process / heme B 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 A biosynthetic process / heme B 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
COPROPORPHYRINOGEN III / Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 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 1.3Mar 12, 2014Group: Non-polymer description
Revision 1.4Oct 27, 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 1.5Aug 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4342
Polymers40,7741
Non-polymers6611
Water6,503361
1
A: Uroporphyrinogen Decarboxylase
hetero molecules

A: Uroporphyrinogen Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8694
Polymers81,5472
Non-polymers1,3222
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)102.680, 102.680, 73.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsURO-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 / E.C.4.1.1.37 / URO-D / UPD


Mass: 40773.730 Da / Num. of mol.: 1 / Mutation: D86G
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: 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.: 361 / 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: 2.36 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 294 K / Method: liquid diffusion / pH: 6.5
Details: PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 1.5 M citrate, pH 6.5, LIQUID ...Details: PBG, PBG-D and U3S were added to the protein solution in an anaerobic chamber. URO-D was active under these conditions, converting uro'gen-III to cop'gen-III. 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
60.1MES1reservoirpH6.0

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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: 1.7→87.71 Å / Num. all: 47218 / Num. obs: 47218 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.232 / % possible all: 88
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 95.7 % / Num. measured all: 230692
Reflection shell
*PLUS
% possible obs: 87.5 %

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Processing

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

1uro


Resolution: 1.7→87.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.34 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20004 1187 2.5 %RANDOM
Rwork0.16944 ---
all0.17019 47218 --
obs0.17019 45924 95.76 %-
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: 22.484 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.53 Å20 Å2
2---1.05 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 48 361 3203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213095
X-RAY DIFFRACTIONr_bond_other_d0.0020.022838
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9774231
X-RAY DIFFRACTIONr_angle_other_deg0.88736583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155388
X-RAY DIFFRACTIONr_chiral_restr0.0980.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023558
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02659
X-RAY DIFFRACTIONr_nbd_refined0.2280.2769
X-RAY DIFFRACTIONr_nbd_other0.240.23497
X-RAY DIFFRACTIONr_nbtor_other0.0840.21811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3160.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3520.239
X-RAY DIFFRACTIONr_mcbond_it0.9591.51881
X-RAY DIFFRACTIONr_mcangle_it1.64123043
X-RAY DIFFRACTIONr_scbond_it2.51531214
X-RAY DIFFRACTIONr_scangle_it4.0624.51188
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.226 150
Rwork0.147 6216
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.2 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.547
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å

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