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- PDB-4fn6: Structural Characterization of Thiaminase type II TenA from Staph... -

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Basic information

Entry
Database: PDB / ID: 4fn6
TitleStructural Characterization of Thiaminase type II TenA from Staphylococcus aureus
Componentsthiaminase-2
KeywordsTRANSCRIPTION / alpha-helix / thiaminase / Vitamin B1 / bi-functional enzyme / cleavage of thiamine into HMP and THZ / deamination of amino-pyrimidine to HMP in S.aureus / HYDROLASE
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process
Similarity search - Function
Thiaminase II / : / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsBegum, A. / Drebes, J. / Perbandt, M. / Wrenger, C. / Betzel, C.
CitationJournal: TO BE PUBLISHED
Title: Structural Characterization of Thiaminase type II TenA from Staphylococcus aureus
Authors: Begum, A. / Drebes, J. / Perbandt, M. / Wrenger, C. / Betzel, C.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thiaminase-2
B: thiaminase-2
C: thiaminase-2
D: thiaminase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,68717
Polymers107,7874
Non-polymers90013
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-60 kcal/mol
Surface area37970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.276, 104.061, 109.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
thiaminase-2 / Thiaminase II


Mass: 26946.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: tenA, SAR2183 / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3) / References: UniProt: Q6GEY1, aminopyrimidine aminohydrolase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28%(w/v) PEG 3500, 0.2 M sodium acetate and 0.1 M Tris HCl buffer pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 13, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.69→30 Å / Num. obs: 31741 / % possible obs: 95.3 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 3.3

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NO6

3no6


Resolution: 2.69→29.872 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 2002 6.32 %Random
Rwork0.2131 ---
obs0.2159 31701 94.95 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.771 Å2 / ksol: 0.297 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.8901 Å2-0 Å20 Å2
2---7.2455 Å2-0 Å2
3---0.3554 Å2
Refinement stepCycle: LAST / Resolution: 2.69→29.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 60 81 7569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017681
X-RAY DIFFRACTIONf_angle_d1.22310342
X-RAY DIFFRACTIONf_dihedral_angle_d19.5462871
X-RAY DIFFRACTIONf_chiral_restr0.0821089
X-RAY DIFFRACTIONf_plane_restr0.0051331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6898-2.7570.41081360.33082046X-RAY DIFFRACTION94
2.757-2.83150.36841520.30152132X-RAY DIFFRACTION97
2.8315-2.91480.33321350.29432134X-RAY DIFFRACTION97
2.9148-3.00880.33691470.30642125X-RAY DIFFRACTION97
3.0088-3.11620.32531310.26962130X-RAY DIFFRACTION96
3.1162-3.24080.25881370.24412141X-RAY DIFFRACTION96
3.2408-3.38810.24051510.23292119X-RAY DIFFRACTION96
3.3881-3.56650.26471410.2222130X-RAY DIFFRACTION95
3.5665-3.78950.30911420.2112121X-RAY DIFFRACTION96
3.7895-4.08150.25171560.19822112X-RAY DIFFRACTION95
4.0815-4.4910.22521320.1722120X-RAY DIFFRACTION94
4.491-5.1380.19341420.16322116X-RAY DIFFRACTION94
5.138-6.46250.22851540.21242112X-RAY DIFFRACTION93
6.4625-29.87360.23641460.18172161X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: -1.2018 Å / Origin y: 18.8541 Å / Origin z: -25.8506 Å
111213212223313233
T0.206 Å2-0.0201 Å2-0.0012 Å2-0.1733 Å2-0.0207 Å2--0.2292 Å2
L0.4203 °2-0.124 °2-0.2844 °2-0.3501 °20.0988 °2--0.4262 °2
S0.0037 Å °-0.0051 Å °0.0004 Å °0.0134 Å °-0.0595 Å °0.1476 Å °0.0393 Å °0.0059 Å °-0 Å °
Refinement TLS groupSelection details: all

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