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- PDB-2dbs: Crystal structure of a hypothetical protein TTHC002 from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 2dbs
TitleCrystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8
Componentshypothetical protein TTHC002
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / TT2175 / TTHC002 / extremely thermophilic bacteria / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyTrna Endonuclease; Chain: A, domain 1 - #20 / TTHC002-like / Protein of unknown function DUF5647 / Family of unknown function (DUF5647) / Trna Endonuclease; Chain: A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Fusatomi, E. / Akasaka, R. / Bessho, Y. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein TTHC002 from Thermus thermophilus HB8
Authors: Yoshikawa, S. / Arai, R. / Kamo-Uchikubo, T. / Fusatomi, E. / Akasaka, R. / Bessho, Y. / Murayama, K. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionDec 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2006Provider: 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 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 30, 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 TTHC002
B: hypothetical protein TTHC002


Theoretical massNumber of molelcules
Total (without water)20,3032
Polymers20,3032
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-23 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.145, 41.145, 87.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein hypothetical protein TTHC002


Mass: 10151.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHC002 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pRARE / References: UniProt: Q5SGN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES-Na, 1.25M Lithium Sulfate, pH 7.0, 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: 0.97924, 0.97957, 0.96000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2005 / Details: Two dimensional focusing mirror
RadiationMonochromator: Si double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979571
30.961
ReflectionResolution: 2→50 Å / Num. obs: 10858 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 24 Å2 / Rsym value: 0.073 / Χ2: 1.017 / Net I/σ(I): 13.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.05 / Num. unique all: 912 / Rsym value: 0.246 / Χ2: 1.011 / % possible all: 80.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→36 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.467. THE R-FACTOR IS 0.2561 AND THE R-FREE IS 0.2712 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 863 9.69 %RANDOM
Rwork0.2561 ---
obs-8908 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.259 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 43.498 Å2
Baniso -1Baniso -2Baniso -3
1--6.762 Å2-5.125 Å20 Å2
2---6.762 Å20 Å2
3---13.524 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.1→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 0 19 1299
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0108
X-RAY DIFFRACTIONc_angle_deg1.997
X-RAY DIFFRACTIONc_dihedral_angle_d24.37
X-RAY DIFFRACTIONc_improper_angle_d1.918
X-RAY DIFFRACTIONc_mcbond_it1.2071.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it1.5112
X-RAY DIFFRACTIONc_scangle_it2.4122.5
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3998 85 9.92 %
Rwork0.3774 772 -
obs-857 71.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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