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- PDB-1wk2: Crystal structure of a hypothetical protein from thermus thermoph... -

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Basic information

Entry
Database: PDB / ID: 1wk2
TitleCrystal structure of a hypothetical protein from thermus thermophilus HB8
ComponentsHYPOTHETICAL PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyHypothetical protein. / ASCH / ASCH domain / ASCH domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA-like superfamily / Roll / Mainly Beta / ASCH domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAgari, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein from thermus thermophilus HB8
Authors: Agari, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 30, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2004Provider: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,1451
Polymers14,1451
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: HYPOTHETICAL PROTEIN

A: HYPOTHETICAL PROTEIN


Theoretical massNumber of molelcules
Total (without water)28,2902
Polymers28,2902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2310 Å2
ΔGint-23 kcal/mol
Surface area10150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.583, 55.846, 43.186
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HYPOTHETICAL PROTEIN


Mass: 14145.099 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SM30
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 44.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 23% PEG3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
1,2,31
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97913, 0.9, 0.97942
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 17, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si Double CrystalMADMx-ray1
2Si Double CrystalMADMx-ray1
3Si Double CrystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.91
30.979421
ReflectionResolution: 1.9→43 Å / Biso Wilson estimate: 30.1 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.78 Å / Rfactor Rfree error: 0.018 / Data cutoff high absF: 1159702.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.389 451 10.6 %RANDOM
Rwork0.327 ---
all0.336 ---
obs0.344 4268 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0321 Å2 / ksol: 0.443893 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.01 Å20 Å21.27 Å2
2--11.81 Å20 Å2
3----2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms683 0 0 45 728
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.463 77 10.6 %
Rwork0.373 650 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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