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- PDB-3d8t: Thermus thermophilus Uroporphyrinogen III Synthase -

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Basic information

Entry
Database: PDB / ID: 3d8t
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
ACETATE ION / Uroporphyrinogen-III synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 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 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9896
Polymers62,7532
Non-polymers2364
Water10,773598
1
A: Uroporphyrinogen-III synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5544
Polymers31,3761
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uroporphyrinogen-III synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4352
Polymers31,3761
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.750, 89.957, 74.981
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uroporphyrinogen-III synthase


Mass: 31376.426 Da / Num. of mol.: 2
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8000, MgCl2, Tris-HCl, pH 8.5, 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: 1.6→50 Å / Num. obs: 58034 / Rsym value: 0.041 / Net I/σ(I): 30.3
Reflection shellResolution: 1.6→1.66 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.351

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.6→34.03 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.776 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3324 5.1 %RANDOM
Rwork0.19 ---
obs0.192 48973 94.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20.05 Å2
2---0.5 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 16 598 4680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224140
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4092.0145626
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1595541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.28322.102176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3931550
X-RAY DIFFRACTIONr_chiral_restr0.0970.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22058
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22787
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2390
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.245
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4831.52689
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.25824172
X-RAY DIFFRACTIONr_scbond_it3.05131611
X-RAY DIFFRACTIONr_scangle_it4.5524.51450
X-RAY DIFFRACTIONr_rigid_bond_restr1.75334300
X-RAY DIFFRACTIONr_sphericity_free6.143466
X-RAY DIFFRACTIONr_sphericity_bonded8.97534047
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 129 -
Rwork0.252 2733 -
obs--55.56 %

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