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- PDB-7jgt: Crystal Structure of FN3tt -

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Basic information

Entry
Database: PDB / ID: 7jgt
TitleCrystal Structure of FN3tt
ComponentsFibronectin type-III domain-containing protein
KeywordsSTRUCTURAL PROTEIN / Hyperthermal stability / Surface Salt Bridges
Function / homology
Function and homology information


IPT/TIG domain / ig-like, plexins, transcription factors / IPT domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Fibronectin type-III domain-containing protein
Similarity search - Component
Biological speciesCaldanaerobacter subterraneus subsp. tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
Model detailsCrystal Structure of FN3tt, a Fibronectin-like Domain from T. tengcongensis
AuthorsLuo, J. / Malia, T.J.
CitationJournal: Proteins / Year: 2022
Title: Surface salt bridges contribute to the extreme thermal stability of an FN3-like domain from a thermophilic bacterium.
Authors: Boucher, L. / Somani, S. / Negron, C. / Ma, W. / Jacobs, S. / Chan, W. / Malia, T. / Obmolova, G. / Teplyakov, A. / Gilliland, G.L. / Luo, J.
History
DepositionJul 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Apr 3, 2024Group: 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: Fibronectin type-III domain-containing protein


Theoretical massNumber of molelcules
Total (without water)11,3221
Polymers11,3221
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.530, 38.530, 105.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-172-

HOH

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Components

#1: Protein Fibronectin type-III domain-containing protein


Mass: 11321.529 Da / Num. of mol.: 1 / Fragment: FN3-like Domain, residues 1458-1547 / Mutation: T68C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (bacteria)
Strain: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / Gene: TTE0165 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RD81
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 1.73 Å3/Da / Density % sol: 28.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M MES pH 6.5, 28% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 18, 2007 / Details: mirrors
RadiationMonochromator: OsmicTM VariMaxTM confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→31.11 Å / Num. obs: 6681 / % possible obs: 98.3 % / Redundancy: 24.13 % / Biso Wilson estimate: 27.131 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.065 / Χ2: 0.94 / Net I/σ(I): 38.63 / Num. measured all: 161213 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9514.5380.3228.8558155024000.9650.33379.7
1.95-218.5460.25212.5784204694540.9860.25996.8
2-2.0624.3830.20718.07109484494490.9920.212100
2.06-2.1226.1740.18419.86118574534530.9960.187100
2.12-2.1926.6720.16123.32116294364360.9960.165100
2.19-2.2725.7280.13726.16113464414410.9980.14100
2.27-2.3627.2010.12528.68105543883880.9980.127100
2.36-2.4526.0050.10733.25104024004000.9980.11100
2.45-2.5626.3090.10732.13102873913910.9980.109100
2.56-2.6926.6690.0938.3393343503500.9990.092100
2.69-2.8325.880.07742.5592393573570.9990.079100
2.83-325.7640.0625085023303300.9990.063100
3-3.2124.8750.05557.2981343273270.9990.056100
3.21-3.4724.9860.0565.6371962882880.9990.051100
3.47-3.824.2990.04669.4966582742740.9990.047100
3.8-4.2523.0590.04374.67585725425410.044100
4.25-4.9122.7620.03977.88516722722710.039100
4.91-6.0122.680.03676.79446819719710.037100
6.01-8.521.5940.03875.05345516016010.038100
8.5-31.1118.5240.03971.2819451061050.9990.0499.1

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rosetta generated

Resolution: 1.9→31.11 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2335 673 10.07 %
Rwork0.1768 6008 -
obs0.1826 6681 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.19 Å2 / Biso mean: 22.8862 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 1.9→31.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms731 0 0 88 819
Biso mean---31 -
Num. residues----92
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-2.050.26991250.18651078120391
2.05-2.250.25311310.181911881319100
2.25-2.580.2891330.187112001333100
2.58-3.250.22011360.187212241360100
3.25-31.110.21031480.164813181466100

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