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- PDB-7wwn: Structure of hypothetical protein TTHA1873 from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 7wwn
TitleStructure of hypothetical protein TTHA1873 from Thermus thermophilus with Potassium mercuric iodide
Componentshypothetical protein TTHA1873
KeywordsUNKNOWN FUNCTION
Function / homologymetal ion binding / tetraiodomercurate(2-) / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.05 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 1.0Apr 6, 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 1.2May 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 TTHA1873
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0978
Polymers18,4761
Non-polymers3,6217
Water1,35175
1
A: hypothetical protein TTHA1873
hetero molecules

A: hypothetical protein TTHA1873
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,19516
Polymers36,9522
Non-polymers7,24214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2350 Å2
ΔGint-61 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.570, 42.570, 156.049
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein hypothetical protein TTHA1873


Mass: 18476.184 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-72I / tetraiodomercurate(2-)


Mass: 708.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: HgI4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.91 Å3/Da / Density % sol: 35.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 0.1 M Tris pH 8.5 and 3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→52.02 Å / Num. obs: 8938 / % possible obs: 89.6 % / Redundancy: 22.6 % / CC1/2: 0.998 / Net I/σ(I): 8.8
Reflection shellResolution: 2.03→2.09 Å / Num. unique obs: 195 / CC1/2: 0.969

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→39.04 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.841 / SU B: 4.233 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 413 4.6 %RANDOM
Rwork0.2041 ---
obs0.2066 8490 92.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 48.26 Å2 / Biso mean: 10.928 Å2 / Biso min: 0.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 2.05→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 30 75 1283
Biso mean--22.99 11.78 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141086
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6611689
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5622503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8475157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73522.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21415157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.568156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02274
LS refinement shellResolution: 2.053→2.107 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 17 -
Rwork0.22 444 -
all-461 -
obs--66.24 %

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