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- PDB-2ei5: Crystal Structure of Hypothetical protein(TTHA0061) from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 2ei5
TitleCrystal Structure of Hypothetical protein(TTHA0061) from Thermus thermophilus
ComponentsHypothetical protein TTHA0061Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Hypothetical protein / Thermus thermophilus / TTHA0061 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsNiwa, H. / Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical protein(TTHA0061) from Thermus thermophilus
Authors: Niwa, H. / Kumarevel, T.S. / Kuramitsu, S. / Yokoyama, S.
History
DepositionMar 12, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8943
Polymers23,6852
Non-polymers2091
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-20 kcal/mol
Surface area11120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.094, 48.094, 150.631
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hypothetical protein TTHA0061 / Hypothesis


Mass: 11842.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TTHA0061 / Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SM82
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 28% PEG MME2000, 0.1M Bis-Tris pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Sep 30, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. all: 15964 / Num. obs: 15964 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.239 / Num. unique all: 1580 / % possible all: 98.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EBG

2ebg


Resolution: 1.88→41.65 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1047770.47 / 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
Rfree0.241 793 5 %RANDOM
Rwork0.201 ---
all0.203 15964 --
obs0.201 15910 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7388 Å2 / ksol: 0.328653 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å22.65 Å20 Å2
2--0.66 Å20 Å2
3----1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.88→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 14 150 1829
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 1.88→2 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 137 5.3 %
Rwork0.232 2453 -
obs--96.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3btb.parambtb.top

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