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- PDB-3re1: Crystal structure of uroporphyrinogen III synthase from Pseudomon... -

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Basic information

Entry
Database: PDB / ID: 3re1
TitleCrystal structure of uroporphyrinogen III synthase from Pseudomonas syringae pv. tomato DC3000
ComponentsUroporphyrinogen-III synthetase
KeywordsLYASE / HemD-like family / uroporphyrinogen III synthase / HMB
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III biosynthetic process / protoporphyrinogen IX biosynthetic process
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 speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsChang, W.R. / Li, M. / Peng, S.X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of uroporphyrinogen III synthase from Pseudomonas syringae pv. tomato DC3000
Authors: Peng, S.X. / Zhang, H. / Gao, Y. / Pan, X. / Cao, P. / Li, M. / Chang, W.R.
History
DepositionApr 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 synthetase
B: Uroporphyrinogen-III synthetase


Theoretical massNumber of molelcules
Total (without water)58,6452
Polymers58,6452
Non-polymers00
Water4,954275
1
A: Uroporphyrinogen-III synthetase


Theoretical massNumber of molelcules
Total (without water)29,3231
Polymers29,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uroporphyrinogen-III synthetase


Theoretical massNumber of molelcules
Total (without water)29,3231
Polymers29,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.668, 67.455, 112.035
Angle α, β, γ (deg.)90.00, 94.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uroporphyrinogen-III synthetase


Mass: 29322.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: hemD / Plasmid: pHAT2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q88B90, uroporphyrinogen-III synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% PEG3350, 0.2M tri-Na citrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 19467 / Num. obs: 19409 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.16 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNS1.2refinement
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7836 / SU ML: 0.34 / σ(F): 0 / Phase error: 27.88 / Stereochemistry target values: ML / Details: The structure was refined also with CNS 1.2.
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 1003 5.18 %RANDOM
Rwork0.2179 ---
obs0.2187 19373 99.27 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.765 Å2 / ksol: 0.301 e/Å3
Displacement parametersBiso max: 96 Å2 / Biso mean: 45.608 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1-21.6843 Å20 Å2-16.3884 Å2
2---12.499 Å20 Å2
3----6.0197 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3855 0 0 275 4130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133944
X-RAY DIFFRACTIONf_angle_d1.4655393
X-RAY DIFFRACTIONf_chiral_restr0.091620
X-RAY DIFFRACTIONf_plane_restr0.009708
X-RAY DIFFRACTIONf_dihedral_angle_d16.0931457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.63180.34631440.2832489263396
2.6318-2.79650.29941330.286226312764100
2.7965-3.01230.29641500.276126082758100
3.0123-3.3150.23341290.23926482777100
3.315-3.79380.25171500.221926592809100
3.7938-4.77640.18181460.18326562802100
4.7764-29.15560.19461510.17712679283099

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