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- PDB-1yak: Complex of Bacillus subtilis TenA with 4-amino-2-methyl-5-hydroxy... -

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Basic information

Entry
Database: PDB / ID: 1yak
TitleComplex of Bacillus subtilis TenA with 4-amino-2-methyl-5-hydroxymethylpyrimidine
ComponentsTranscriptional activator tenA
KeywordsTRANSCRIPTION / thiaminase
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / cytosol
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
4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE / Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsToms, A.V. / Haas, A.L. / Park, J.-H. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2005
Title: Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II.
Authors: Toms, A.V. / Haas, A.L. / Park, J.H. / Begley, T.P. / Ealick, S.E.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_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

Downloads & links

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Assembly

Deposited unit
A: Transcriptional activator tenA
B: Transcriptional activator tenA
C: Transcriptional activator tenA
D: Transcriptional activator tenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8378
Polymers122,2804
Non-polymers5574
Water3,423190
1
A: Transcriptional activator tenA
B: Transcriptional activator tenA
hetero molecules

A: Transcriptional activator tenA
B: Transcriptional activator tenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8378
Polymers122,2804
Non-polymers5574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9510 Å2
ΔGint-46 kcal/mol
Surface area34620 Å2
MethodPISA, PQS
2
C: Transcriptional activator tenA
D: Transcriptional activator tenA
hetero molecules

C: Transcriptional activator tenA
D: Transcriptional activator tenA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8378
Polymers122,2804
Non-polymers5574
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area9870 Å2
ΔGint-46 kcal/mol
Surface area34270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)82.958, 82.928, 296.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a tetramer. The asymmetric unit contains 2 half biological units.

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Components

#1: Protein
Transcriptional activator tenA


Mass: 30569.998 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: tenA / Plasmid: pDESTF1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25052
#2: Chemical
ChemComp-HMH / 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE


Mass: 139.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H9N3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.7 M 1,6-hexanediol, 10 mM MgCl2, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 33460 / Num. obs: 33417 / % possible obs: 93.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 28.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 21.3
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4072 / Rsym value: 0.264 / % possible all: 68.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YAF

1yaf


Resolution: 2.5→49.39 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3184563.21 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1681 5 %RANDOM
Rwork0.217 ---
all0.222 33460 --
obs0.217 33417 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.49 Å2 / ksol: 0.358823 e/Å3
Displacement parametersBiso mean: 62.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.55 Å20 Å20 Å2
2--13.67 Å20 Å2
3----29.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 40 190 7460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 197 4.8 %
Rwork0.307 3875 -
obs-4072 68.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4HMP.PARAMHMP.TOP

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