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- PDB-7wrk: Structure of hypothetical protein TTHA1873 from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 7wrk
TitleStructure of hypothetical protein TTHA1873 from Thermus thermophilus
Componentshypothetical protein TTHA1873
KeywordsUNKNOWN FUNCTION
Function / homologymetal ion binding / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.78 Å
AuthorsYuvaraj, I. / Santosh, K.C. / 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
DepositionJan 27, 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 1.2May 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)18,5563
Polymers18,4761
Non-polymers802
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area6930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.180, 42.180, 156.890
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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.89 Å3/Da / Density % sol: 34.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / 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: 1.78→52.3 Å / Num. obs: 14566 / % possible obs: 100 % / Redundancy: 11.8 % / CC1/2: 0.995 / Net I/σ(I): 12.6
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 804 / CC1/2: 0.98

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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: 1.78→40.77 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.953 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 732 5.1 %RANDOM
Rwork0.1624 ---
obs0.1642 13757 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.15 Å2 / Biso mean: 13.743 Å2 / Biso min: 8.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å2-0 Å2-0 Å2
2--0.26 Å2-0 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.78→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 2 125 1308
Biso mean--10.99 23.24 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0141087
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6621665
X-RAY DIFFRACTIONr_angle_other_deg1.6031.5622506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4115159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75322.72755
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.8415157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.654156
X-RAY DIFFRACTIONr_chiral_restr0.0940.2168
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
LS refinement shellResolution: 1.78→1.823 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.219 47 -
Rwork0.195 983 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 20.7263 Å / Origin y: 16.5029 Å / Origin z: 10.3197 Å
111213212223313233
T0.0046 Å2-0.0042 Å2-0.0029 Å2-0.0134 Å20.0089 Å2--0.006 Å2
L0.8706 °2-0.3661 °2-0.037 °2-1.4224 °20.2973 °2--1.5458 °2
S0.0261 Å °-0.0079 Å °-0.0135 Å °0.0542 Å °-0.0318 Å °-0.014 Å °0.0189 Å °0.0088 Å °0.0057 Å °

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