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- PDB-2ebe: Crystal structure of Lys11 to Met mutant of hypothetical protein ... -

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Basic information

Entry
Database: PDB / ID: 2ebe
TitleCrystal structure of Lys11 to Met mutant of hypothetical protein from Thermus thermophilus
ComponentsHypothetical protein TTHA0061
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / TTHA0061 / thermus thermophilus / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyProtein of unknown function (DUF3208) / Protein of unknown function DUF3208 / Protein of unknown function (DUF3208) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / DUF3208 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Lys11 to Met mutant of hypothetical protein from Thermus thermophilus
Authors: Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S.
History
DepositionFeb 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein TTHA0061
B: Hypothetical protein TTHA0061


Theoretical massNumber of molelcules
Total (without water)23,7212
Polymers23,7212
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area11530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.460, 69.710, 73.990
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 TTHA0061


Mass: 11860.635 Da / Num. of mol.: 2 / Mutation: L11M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0061 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SM82
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 25% PEG 2000 MME, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 7, 2006
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 22011 / Num. obs: 22011 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.281 / Num. unique all: 2142 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→19.68 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1165474.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1098 5 %RANDOM
Rwork0.225 ---
obs0.225 21931 99.9 %-
all-22011 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.706 Å2 / ksol: 0.356397 e/Å3
Displacement parametersBiso mean: 29.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.33 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 0 210 1888
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.322
X-RAY DIFFRACTIONc_scangle_it3.42.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 177 4.9 %
Rwork0.235 3408 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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