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- PDB-2ywa: Crystal structure of uncharacterized conserved protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 2ywa
TitleCrystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
ComponentsHypothetical protein TTHA0048
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / uncharacterized conserved protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyProbable ribonuclease HepT / Nucleotidyltransferase substrate binding protein like / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Nucleotidyltransferase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Thermus thermophilus HB8
Authors: Kitamura, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionApr 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein TTHA0048
B: Hypothetical protein TTHA0048
C: Hypothetical protein TTHA0048
D: Hypothetical protein TTHA0048


Theoretical massNumber of molelcules
Total (without water)56,1834
Polymers56,1834
Non-polymers00
Water00
1
A: Hypothetical protein TTHA0048
B: Hypothetical protein TTHA0048


Theoretical massNumber of molelcules
Total (without water)28,0922
Polymers28,0922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Hypothetical protein TTHA0048
D: Hypothetical protein TTHA0048


Theoretical massNumber of molelcules
Total (without water)28,0922
Polymers28,0922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.760, 121.760, 322.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Hypothetical protein TTHA0048 / uncharacterized conserved protein


Mass: 14045.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM95
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: 6.14 Å3/Da / Density % sol: 79.97 % / Description: the file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.5M NaFormate 0.1M Tris-HCl pH8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Feb 6, 2004
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.2→44.28 Å / Num. obs: 44105 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 16.1
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 19.37 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2340 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WTY

1wty


Resolution: 3.2→44.13 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 216963.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2218 5 %RANDOM
Rwork0.216 ---
obs0.216 44078 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.7125 Å2 / ksol: 0.383684 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1-5.02 Å221.68 Å20 Å2
2--5.02 Å20 Å2
3----10.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.2→44.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3815 0 0 0 3815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 354 4.8 %
Rwork0.272 6981 -
obs--99.8 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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