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- PDB-7wwo: Dimer form of hypothetical protein TTHA1873 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 7wwo
TitleDimer form of hypothetical protein TTHA1873 from Thermus thermophilus
Componentshypothetical protein TTHA1873
KeywordsUNKNOWN FUNCTION / Hypothetical protein
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsYuvaraj, I. / Sekar, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Structure of the hypothetical protein TTHA1873 from Thermus thermophilus.
Authors: Yuvaraj, I. / Chaudhary, S.K. / Jeyakanthan, J. / Sekar, K.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTHA1873
B: hypothetical protein TTHA1873
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1136
Polymers36,9522
Non-polymers1604
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-60 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.422, 90.422, 141.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein hypothetical protein TTHA1873


Mass: 18476.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHA1873
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5SH57
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 60% v/v Tacsimate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0723 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.17→68.63 Å / Num. obs: 18800 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.959 / Net I/σ(I): 5.6
Reflection shellResolution: 2.17→2.24 Å / Num. unique obs: 1575 / CC1/2: 0.906

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7wrk

7wrk


Resolution: 2.17→68.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.034 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 907 4.8 %RANDOM
Rwork0.1858 ---
obs0.1874 17892 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.62 Å2 / Biso mean: 40.727 Å2 / Biso min: 22.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 2.17→68.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 4 60 2404
Biso mean--34.25 46.65 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142156
X-RAY DIFFRACTIONr_angle_refined_deg1.591.663299
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5644964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6185316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68522.593108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57515309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.291512
X-RAY DIFFRACTIONr_chiral_restr0.0630.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
LS refinement shellResolution: 2.17→2.226 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.309 65 -
Rwork0.247 1278 -
obs--99.85 %

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