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- PDB-1udd: TenA homologue protein from P.horikoshii OT3 -

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Basic information

Entry
Database: PDB / ID: 1udd
TitleTenA homologue protein from P.horikoshii OT3
Componentstranscriptional regulator
KeywordsLIPID BINDING PROTEIN / Helix-bundle
Function / homology
Function and homology information


thiaminase activity / thiamine metabolic 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
218aa long hypothetical transcriptional regulator
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.15 Å
AuthorsItou, H. / Yao, M. / Watanabe, N. / Tanaka, I.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure analysis of PH1161 protein, a transcriptional activator TenA homologue from the hyperthermophilic archaeon Pyrococcus horikoshii.
Authors: Itou, H. / Yao, M. / Watanabe, N. / Tanaka, I.
History
DepositionApr 28, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator
B: transcriptional regulator
C: transcriptional regulator
D: transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)106,4834
Polymers106,4834
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-53 kcal/mol
Surface area35550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.8, 116.8, 70.97
Angle α, β, γ (deg.)90, 90, 120
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
transcriptional regulator / TenA homologue protein PH1161


Mass: 26620.748 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Plasmid: PET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O58873
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG1000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2002 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. all: 58766 / Num. obs: 58735 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.082 / Net I/σ(I): 7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 8595 / Rsym value: 0.284 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.15→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5723 -random
Rwork0.218 ---
all-58310 --
obs-58170 100 %-
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7066 0 0 155 7221
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.195
X-RAY DIFFRACTIONc_dihedral_angle_d18.12
LS refinement shellResolution: 2.15→2.23 Å
RfactorNum. reflection% reflection
Rfree0.301 592 -
Rwork0.257 --
obs-5214 89.8 %

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