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- PDB-1wwm: Crystal Structure of Conserved Hypothetical Protein TT2028 from a... -

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Basic information

Entry
Database: PDB / ID: 1wwm
TitleCrystal Structure of Conserved Hypothetical Protein TT2028 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8
Componentshypothetical protein TT2028
KeywordsTRANSCRIPTION / TenA/Thi-4 family / putative transctiption activator / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyHeme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / Transcriptional regulator
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.61 Å
AuthorsMizohata, E. / Ushikoshi-Nakayama, R. / Terada, T. / Murayama, K. / Sakai, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of TT2028 from an Extremely Thermophilic Bacterium Thermus thermophilus HB8
Authors: Mizohata, E. / Ushikoshi-Nakayama, R. / Terada, T. / Murayama, K. / Sakai, H. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionJan 7, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TT2028
B: hypothetical protein TT2028


Theoretical massNumber of molelcules
Total (without water)44,5362
Polymers44,5362
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.210, 101.121, 102.913
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein TT2028


Mass: 22268.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SLX4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.43 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: MES, PEG8000, magnesium acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.96200, 0.97904, 0.97932
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9621
20.979041
30.979321
ReflectionResolution: 2.6→50 Å / Num. obs: 24268 / Biso Wilson estimate: 13.5 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.61→30.65 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 180963.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1147 4.7 %RANDOM
Rwork0.234 ---
obs0.234 24246 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8882 Å2 / ksol: 0.360115 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.71 Å20 Å20 Å2
2--8.45 Å20 Å2
3----12.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.61→30.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2827 0 0 116 2943
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
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
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 144 4.2 %
Rwork0.322 3269 -
obs--80.4 %

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