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- PDB-2thi: THIAMINASE I FROM BACILLUS THIAMINOLYTICUS -

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Basic information

Entry
Database: PDB / ID: 2thi
TitleTHIAMINASE I FROM BACILLUS THIAMINOLYTICUS
ComponentsTHIAMINASE I
KeywordsTRANSFERASE / THIAMINE 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
Biological speciesPaenibacillus thiaminolyticus (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 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
DepositionSep 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: THIAMINASE I
B: THIAMINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4253
Polymers84,3292
Non-polymers961
Water68538
1
A: THIAMINASE I


Theoretical massNumber of molelcules
Total (without water)42,1641
Polymers42,1641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: THIAMINASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2612
Polymers42,1641
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.700, 120.500, 76.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999973, -0.000107, 0.007335), (0.0001, -0.999999, -0.000951), (0.007335, -0.00095, 0.999972)
Vector: 41.26728, 120.45187, -0.23723)

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Components

#1: Protein THIAMINASE I


Mass: 42164.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus thiaminolyticus (bacteria)
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.: 38 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION ON NONCRYSTALLOGRAPHIC TWO-FOLD

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 23741 / % possible obs: 83 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rsym value: 0.05
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.05

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Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.842refinement
ADSCdata collection
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→30.5 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.275 -5 %RANDOM
Rwork0.195 ---
obs0.195 23430 83 %-
Refinement stepCycle: LAST / Resolution: 2.5→30.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5716 0 5 38 5759
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.5
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Software
*PLUS
Name: X-PLOR / Version: 3.842 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.27

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