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- PDB-1r3q: Uroporphyrinogen Decarboxylase in complex with coproporphyrinogen-I -

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Basic information

Entry
Database: PDB / ID: 1r3q
TitleUroporphyrinogen Decarboxylase in complex with coproporphyrinogen-I
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
COPROPORPHYRINOGEN I / CARBON DIOXIDE / Uroporphyrinogen decarboxylase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uroporphyrinogen Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5373
Polymers40,8321
Non-polymers7052
Water5,873326
1
A: Uroporphyrinogen Decarboxylase
hetero molecules

A: Uroporphyrinogen Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0736
Polymers81,6642
Non-polymers1,4104
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)102.930, 102.930, 74.510
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe asymmetric unit contains one URO-D monomer. URO-D is a dimer. The dimer is formed by the crystallographic 2-fold operator.

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Components

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


Mass: 40831.766 Da / Num. of mol.: 1
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-1CP / COPROPORPHYRINOGEN I / Coproporphyrinogen I


Mass: 660.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H44N4O8
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.5 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 294 K / Method: liquid diffusion / pH: 6.5
Details: Crystallization of URO-D in complex with coproporphyrinogen required crystallization in an anaerobic chamber with PBG and PBG-D added to the solution for the generation of uroporphyrinogen ...Details: Crystallization of URO-D in complex with coproporphyrinogen required crystallization in an anaerobic chamber with PBG and PBG-D added to the solution for the generation of uroporphyrinogen in-situ. URO-D was active under these conditions, creating coproporphyrinogen. 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: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 50593 / Num. obs: 50593 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 13
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.485 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.7 Å / % possible obs: 99.6 % / Num. measured all: 270866
Reflection shell
*PLUS
% possible obs: 99.8 %

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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: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.724 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19248 1245 2.5 %RANDOM
Rwork0.16684 ---
all0.16749 50593 --
obs0.16749 48908 99.54 %-
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: 25.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.27 Å2-0.63 Å20 Å2
2---1.27 Å20 Å2
3---1.9 Å2
Refinement stepCycle: LAST / Resolution: 1.7→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2802 0 51 326 3179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0213012
X-RAY DIFFRACTIONr_bond_other_d0.0020.022762
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.984106
X-RAY DIFFRACTIONr_angle_other_deg0.88436405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4125372
X-RAY DIFFRACTIONr_chiral_restr0.0960.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023414
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02633
X-RAY DIFFRACTIONr_nbd_refined0.2210.2680
X-RAY DIFFRACTIONr_nbd_other0.2420.23279
X-RAY DIFFRACTIONr_nbtor_other0.0870.21750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.224
X-RAY DIFFRACTIONr_mcbond_it1.0421.51833
X-RAY DIFFRACTIONr_mcangle_it1.91122952
X-RAY DIFFRACTIONr_scbond_it2.97631179
X-RAY DIFFRACTIONr_scangle_it54.51154
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.275 166
Rwork0.217 7098
Software
*PLUS
Version: 5.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.192 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.633
LS refinement shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.79 Å

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