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- PDB-3d8r: Thermus thermophilus Uroporphyrinogen III Synthase -

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Basic information

Entry
Database: PDB / ID: 3d8r
TitleThermus thermophilus Uroporphyrinogen III Synthase
ComponentsUroporphyrinogen-III synthase
KeywordsLYASE / heme biosynthesis
Function / homology
Function and homology information


uroporphyrinogen-III synthase / uroporphyrinogen-III synthase activity / uroporphyrinogen III 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
PHOSPHATE ION / Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSchubert, H.L.
CitationJournal: Biochemistry / Year: 2008
Title: Structure and mechanistic implications of a uroporphyrinogen III synthase-product complex.
Authors: Schubert, H.L. / Phillips, J.D. / Heroux, A. / Hill, C.P.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uroporphyrinogen-III synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7565
Polymers31,3761
Non-polymers3804
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.831, 63.831, 58.584
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Uroporphyrinogen-III synthase


Mass: 31376.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: TT_C0312 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q72KM1, uroporphyrinogen-III synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 1.2 M NaPO4, 0.8 M K2PO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 19472 / % possible obs: 100 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.086 / Χ2: 2.239 / Net I/σ(I): 14.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.027.70.42519551.7351100
2.02-2.17.50.31319411.81100
2.1-2.27.50.23219391.911100
2.2-2.317.70.18819401.9461100
2.31-2.467.60.14919762.0191100
2.46-2.657.60.12419212.0491100
2.65-2.917.60.09419642.1511100
2.91-3.337.50.06719462.4531100
3.33-4.27.60.05219352.9281100
4.2-507.20.05319553.473199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.821 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 914 5.1 %RANDOM
Rwork0.178 ---
obs0.181 18042 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.414 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 20 224 2192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222054
X-RAY DIFFRACTIONr_angle_refined_deg1.2472.0232786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8325262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7422.35385
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23515360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8571523
X-RAY DIFFRACTIONr_chiral_restr0.0810.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211547
X-RAY DIFFRACTIONr_mcbond_it0.7081.51288
X-RAY DIFFRACTIONr_mcangle_it1.39322055
X-RAY DIFFRACTIONr_scbond_it2.5373766
X-RAY DIFFRACTIONr_scangle_it4.4154.5731
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 73 -
Rwork0.188 1259 -
all-1332 -
obs--100 %

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