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- PDB-3thi: THIAMINASE I FROM BACILLUS THIAMINOLYTICUS -

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Basic information

Entry
Database: PDB / ID: 3thi
TitleTHIAMINASE I FROM BACILLUS THIAMINOLYTICUS
ComponentsPROTEIN (THIAMINASE I)
KeywordsTRANSFERASE / THIAMIN DEGRADATION
Function / homology
Function and homology information


thiamine pyridinylase / thiamine pyridinylase activity / thiamine catabolic process / extracellular region
Similarity search - Function
Thiaminase-1 / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCampobasso, N. / Begley, T.P. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structure of thiaminase-I from Bacillus thiaminolyticus at 2.0 A resolution.
Authors: Campobasso, N. / Costello, C.A. / Kinsland, C. / Begley, T.P. / Ealick, S.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and Preliminary X-Ray Analysis of Thiaminase I from Bacillus Thiaminolyticus: Space Group Change Upon Freezing of Crystals
Authors: Campobasso, N. / Begun, J. / Costello, C.A. / Begley, T.P. / Ealick, S.E.
History
DepositionOct 4, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (THIAMINASE I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4892
Polymers41,3931
Non-polymers961
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.500, 117.500, 36.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-380-

SO4

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Components

#1: Protein PROTEIN (THIAMINASE I)


Mass: 41392.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Cellular location: PERIPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P45741, thiamine pyridinylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION ON CRYSTALLOGRAPHIC TWO-FOLD
Sequence detailsTHE SWISS-PROT SEQUENCE CONTAINS A SIGNAL SEQUENCE THAT GETS PROCESSED AT THREE DIFFERENT SITES. ...THE SWISS-PROT SEQUENCE CONTAINS A SIGNAL SEQUENCE THAT GETS PROCESSED AT THREE DIFFERENT SITES. THE NUMBERING OF RESIDUES IN THIS PDB FILE IS CONSISTENT WITH THE PAPER: COSTELLO, ETAL. (1996). JBC, VOL. 271, NO. 7, PP. 3445 - 3452

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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: 2.18 Å3/Da / Density % sol: 44 %
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE (PH = 4.6) 0.2M AMMONIUM SULFATE 30% (W/V) PEG2000
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
250 mMsodium phosphate1drop
32 mMdithiothreitol1drop
42 mMEDTA1drop
50.1-0.2 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir
726-32 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9104
DetectorType: PRINCETON 2K / Detector: CCD / Date: Nov 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9104 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 23741 / % possible obs: 89 % / Redundancy: 6.7 % / Rsym value: 5.6 / Net I/σ(I): 19.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 7.8 / Rsym value: 11.3 / % possible all: 52.2
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 52.2 % / Rmerge(I) obs: 0.113

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.842refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RM TEMP STRUCTURE 2THI

2thi


Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.256 -5 %RANDOM
Rwork0.205 ---
obs0.205 21929 89 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2858 0 3 126 2987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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