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- PDB-1wwi: Crystal structure of ttk003001566 from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1wwi
TitleCrystal structure of ttk003001566 from Thermus Thermophilus HB8
Componentshypothetical protein TTHA1479
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyProtein of unknown function DUF1931 / Domain of unknown function (DUF1931) / Histone, subunit A / Histone, subunit A / Histone-fold / protein heterodimerization activity / Orthogonal Bundle / Mainly Alpha / DUF1931 family protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.58 Å
AuthorsWang, H. / Murayama, K. / Terada, T. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of ttk003001566 from Thermus Thermophilus HB8
Authors: Wang, H. / Murayama, K. / Terada, T. / Chen, L. / Liu, Z.J. / Wang, B.C. / Shirouzu, M. / Kuramitsu, S. / Yokoyama, S.
History
DepositionJan 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 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 TTHA1479


Theoretical massNumber of molelcules
Total (without water)17,0231
Polymers17,0231
Non-polymers00
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: hypothetical protein TTHA1479

A: hypothetical protein TTHA1479


Theoretical massNumber of molelcules
Total (without water)34,0462
Polymers34,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2870 Å2
ΔGint-19 kcal/mol
Surface area13170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)31.448, 107.406, 89.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein hypothetical protein TTHA1479


Mass: 17023.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8 / ATCC 27634 / DSM 579 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SI95
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.2 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG6000, Lithium Nitrate, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793, 0.9795, 0.9686
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
30.96861
ReflectionResolution: 1.58→50 Å / Num. obs: 21115 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 18.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 18.3
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 2029 / Rsym value: 0.181 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.58→30.18 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 467659.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1005 4.8 %RANDOM
Rwork0.186 ---
obs0.186 20800 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.6764 Å2 / ksol: 0.350328 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å20 Å2
2--0.69 Å20 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.58→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 0 140 1328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
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: 1.58→1.68 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.218 150 4.4 %
Rwork0.193 3230 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

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