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- PDB-1wv8: Crystal structure of hypothetical protein TTHA1013 from an extrem... -

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Basic information

Entry
Database: PDB / ID: 1wv8
TitleCrystal structure of hypothetical protein TTHA1013 from an extremely thermophilic bacterium thermus thermophilus HB8
Componentshypothetical protein TTHA1013
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical / novel fold / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTTHA1013-like / Domain of unknown function DUF1902 / Domain of unknown function (DUF1902) / TTHA1013/TTHA0281-like / TTHA1013/TTHA0281-like / 2-Layer Sandwich / Alpha Beta / DUF1902 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMizohata, E. / Hattori, M. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of the hypothetical protein TTHA1013 from Thermus thermophilus HB8
Authors: Hattori, M. / Mizohata, E. / Manzoku, M. / Bessho, Y. / Murayama, K. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 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 TTHA1013


Theoretical massNumber of molelcules
Total (without water)8,0141
Polymers8,0141
Non-polymers00
Water68538
1
A: hypothetical protein TTHA1013

A: hypothetical protein TTHA1013


Theoretical massNumber of molelcules
Total (without water)16,0282
Polymers16,0282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area2320 Å2
ΔGint-15 kcal/mol
Surface area8050 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.897, 51.897, 117.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-85-

HOH

21A-110-

HOH

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Components

#1: Protein hypothetical protein TTHA1013 / TT1413


Mass: 8013.877 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJJ5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.878 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, sodium acetate, PEG4000, Tris-HCl, Sodium chloride, pH 4.6, 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: 0.96300, 0.97911, 0.97937, 1.00000
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 17, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9631
20.979111
30.979371
411
ReflectionResolution: 2.2→50 Å / Num. obs: 5283 / Biso Wilson estimate: 30.3 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→44.95 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 573827.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 285 5.5 %RANDOM
Rwork0.259 ---
obs0.259 5222 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5787 Å2 / ksol: 0.355245 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å2-1.96 Å20 Å2
2--3.19 Å20 Å2
3----6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms541 0 0 38 579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
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: 2.2→2.34 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 36 4.3 %
Rwork0.316 797 -
obs--99.5 %

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