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- PDB-4thi: THIAMINASE I FROM BACILLUS THIAMINOLYTICUS WITH COVALENTLY BOUND ... -

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Basic information

Entry
Database: PDB / ID: 4thi
TitleTHIAMINASE I FROM BACILLUS THIAMINOLYTICUS WITH COVALENTLY BOUND 4-AMINO-2,5-DIMETHYLPYRIMIDINE
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 / : / Thiaminase-1 domain / 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
2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE / Thiaminase-1
Similarity search - Component
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 5, 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 20, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (THIAMINASE I)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7383
Polymers40,5191
Non-polymers2192
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.700, 119.300, 37.300
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-372-

SO4

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Components

#1: Protein PROTEIN (THIAMINASE I)


Mass: 40518.801 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: Chemical ChemComp-PYD / 2,5-DIMETHYL-PYRIMIDIN-4-YLAMINE


Mass: 123.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsSULFATE ION ON CRYSTALLOGRAPHIC TWO-FOLD SG OF CYS IS COVALENTLY BOUND TO THE C6 ATOM OF 4-AMINO- ...SULFATE ION ON CRYSTALLOGRAPHIC TWO-FOLD SG OF CYS IS COVALENTLY BOUND TO THE C6 ATOM OF 4-AMINO-2,5-DIMETHYLPYRIMIDINE
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: 2.29 Å3/Da / Density % sol: 46 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG60001reservoir
20.2 Msodium acetate trihydrate1reservoir
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9104
DetectorType: PRINCETON / Detector: CCD
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: 23969 / % possible obs: 89.2 % / Redundancy: 6.7 % / Rsym value: 0.046 / Net I/σ(I): 31.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 7.2 / Rsym value: 0.15 / % possible all: 54
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 54 % / Rmerge(I) obs: 0.15

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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
Rfree0.258 -5 %RANDOM
Rwork0.211 ---
obs0.211 23256 89.2 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2859 0 12 129 3000
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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