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- PDB-1jr2: Structure of Uroporphyrinogen III Synthase -

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Basic information

Entry
Database: PDB / ID: 1jr2
TitleStructure of Uroporphyrinogen III Synthase
ComponentsUROPORPHYRINOGEN-III SYNTHASE
KeywordsLYASE / Heme biosynthesis / heam biosynthesis
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / response to platinum ion / cellular response to amine stimulus / protoporphyrinogen IX biosynthetic process / cellular response to arsenic-containing substance / Heme biosynthesis / folic acid binding / heme biosynthetic process ...uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / response to platinum ion / cellular response to amine stimulus / protoporphyrinogen IX biosynthetic process / cellular response to arsenic-containing substance / Heme biosynthesis / folic acid binding / heme biosynthetic process / response to antibiotic / mitochondrion / cytosol
Similarity search - Function
Rossmann fold - #10090 / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase / Tetrapyrrole biosynthesis, uroporphyrinogen III synthase superfamily / Uroporphyrinogen-III synthase / Uroporphyrinogen-III synthase HemD / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsMathews, M.A. / Schubert, H.L. / Whitby, F.G. / Alexander, K.J. / Schadick, K. / Bergonia, H.A. / Phillips, J.D. / Hill, C.P.
CitationJournal: EMBO J. / Year: 2001
Title: Crystal structure of human uroporphyrinogen III synthase.
Authors: Mathews, M.A. / Schubert, H.L. / Whitby, F.G. / Alexander, K.J. / Schadick, K. / Bergonia, H.A. / Phillips, J.D. / Hill, C.P.
History
DepositionAug 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Feb 7, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UROPORPHYRINOGEN-III SYNTHASE
B: UROPORPHYRINOGEN-III SYNTHASE


Theoretical massNumber of molelcules
Total (without water)62,3792
Polymers62,3792
Non-polymers00
Water10,251569
1
A: UROPORPHYRINOGEN-III SYNTHASE


Theoretical massNumber of molelcules
Total (without water)31,1891
Polymers31,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UROPORPHYRINOGEN-III SYNTHASE


Theoretical massNumber of molelcules
Total (without water)31,1891
Polymers31,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.852, 59.251, 61.944
Angle α, β, γ (deg.)80.47, 73.32, 88.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein UROPORPHYRINOGEN-III SYNTHASE / Uro'gen III synthase / UROS / UROPORPHYRINOGEN-III COSYNTHETASE / HYDROXYMETHYLBILANE HYDROLYASE ...Uro'gen III synthase / UROS / UROPORPHYRINOGEN-III COSYNTHETASE / HYDROXYMETHYLBILANE HYDROLYASE [CYCLIZING] / UROIIIS


Mass: 31189.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UROS / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+ / References: UniProt: P10746, uroporphyrinogen-III synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 569 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPD, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
220 %MPD1reservoir
3100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 2000
RadiationMonochromator: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 46295 / Num. obs: 43540 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3 % / Rsym value: 0.039 / Net I/σ(I): 22
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1767 / Rsym value: 0.297 / % possible all: 76
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 94 % / Num. measured all: 201469 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 75.8 % / Rmerge(I) obs: 0.327

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.84→58.72 Å / SU B: 10.616 / SU ML: 0.167 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.745 / ESU R Free: 0.158 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25099 2214 5.1 %RANDOM
Rwork0.20041 ---
obs0.2031 41290 93.27 %-
all-41290 --
Displacement parametersBiso mean: 26.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å22.06 Å2-0.58 Å2
2---0.01 Å2-0.82 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.84→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 0 569 4537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_mcbond_it0.0131.444
X-RAY DIFFRACTIONp_mcangle_it1.7232.383
X-RAY DIFFRACTIONp_scbond_it1.372
X-RAY DIFFRACTIONp_scangle_it2.217
LS refinement shellResolution: 1.838→1.886 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 122
Rwork0.245 2296
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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