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- PDB-1tyh: Crystal Structure of Transcriptional Activator tenA from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 1tyh
TitleCrystal Structure of Transcriptional Activator tenA from Bacillus subtilis
ComponentsTranscriptional activator tenA
KeywordsTRANSCRIPTION / all helical structure / tetramer / tenA / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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
Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.54 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Transcriptional Activator tenA from Bacillus subtilis
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionJul 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator tenA
B: Transcriptional activator tenA
D: Transcriptional activator tenA
E: Transcriptional activator tenA


Theoretical massNumber of molelcules
Total (without water)116,3534
Polymers116,3534
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-49 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.430, 58.430, 297.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Transcriptional activator tenA


Mass: 29088.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: TENA, BSU11650 / Production host: Escherichia coli (E. coli) / References: UniProt: P25052
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG 4000, Sodium Citrate, Glycerol, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.97959, 0.97991, 0.94
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2004 / Details: Si Mirrors
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979591
20.979911
30.941
ReflectionResolution: 2.53→50 Å / Num. all: 32993 / Num. obs: 32993 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.8
Reflection shellResolution: 2.53→2.62 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.401 / Num. unique all: 3194 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.54→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A continuous electron density appears between residues ASP 44 and CYS 135. This density might represent either a possible cofactor or a substrate which is unknown at this time and not ...Details: A continuous electron density appears between residues ASP 44 and CYS 135. This density might represent either a possible cofactor or a substrate which is unknown at this time and not modeled. Instead, the density is modeled with discrete water molecules (1, 2, 11, 18, 35, 73, 111, 112 and 113).
RfactorNum. reflection% reflectionSelection details
Rfree0.3039 1572 -RANDOM
Rwork0.2437 ---
obs0.2437 31624 96.9 %-
all-31624 --
Refinement stepCycle: LAST / Resolution: 2.54→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7140 0 0 112 7252
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.235
X-RAY DIFFRACTIONc_bond_d0.0086

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