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- PDB-2ysk: Crystal structure of a hypothetical protein TTHA1432 from Thermus... -

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Basic information

Entry
Database: PDB / ID: 2ysk
TitleCrystal structure of a hypothetical protein TTHA1432 from Thermus thermophilus
ComponentsHypothetical protein TTHA1432
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / conserved hypothetical / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyUncharacterized conserved protein DUF2267 / Protein of unknown function DUF2267 / Uncharacterized conserved protein DUF2267 superfamily / Uncharacterized conserved protein (DUF2267) / Globin-like / Orthogonal Bundle / Mainly Alpha / DUF2267 domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOkamoto, A. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein TTHA1432 from Thermus thermophilus
Authors: Okamoto, A. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 3, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 TTHA1432
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3772
Polymers16,2811
Non-polymers961
Water2,540141
1
A: Hypothetical protein TTHA1432
hetero molecules

A: Hypothetical protein TTHA1432
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7544
Polymers32,5622
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2740 Å2
ΔGint-62.3 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.457, 35.457, 211.966
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Hypothetical protein TTHA1432


Mass: 16280.763 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) / Strain (production host): B834(DE3) / References: UniProt: Q5SIE2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate, 0.08M Ammonium sulfate, 12%w/v PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Mar 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→34.971 Å / Num. obs: 11677 / % possible obs: 99.8 % / Biso Wilson estimate: 7.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 24.68
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 17.66 / Num. unique all: 1153 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→34.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1644090.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 579 5 %RANDOM
Rwork0.206 ---
obs0.206 11587 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.6056 Å2 / ksol: 0.384938 e/Å3
Displacement parametersBiso mean: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å20 Å2
2---2.03 Å20 Å2
3---0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 5 141 1285
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.232
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 91 4.9 %
Rwork0.207 1770 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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