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- PDB-7oom: N-terminal domain of FlSp spidroin from Nephila clavipes -

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Basic information

Entry
Database: PDB / ID: 7oom
TitleN-terminal domain of FlSp spidroin from Nephila clavipes
ComponentsFlagelliform spidroin variant 1
KeywordsSTRUCTURAL PROTEIN / Spider silk / spidroin
Function / homologySpidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Flagelliform spidroin variant 1
Function and homology information
Biological speciesNephila clavipes (spider)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsTars, K. / Metlans, R. / Fridmanis, J. / Jaudzems, K.
Funding support Latvia, 1items
OrganizationGrant numberCountry
European Regional Development Fund1.1.1.1/18/A/004 Latvia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The dimerization mechanism of the N-terminal domain of spider silk proteins is conserved despite extensive sequence divergence.
Authors: Sarr, M. / Kitoka, K. / Walsh-White, K.A. / Kaldmae, M. / Metlans, R. / Tars, K. / Mantese, A. / Shah, D. / Landreh, M. / Rising, A. / Johansson, J. / Jaudzems, K. / Kronqvist, N.
History
DepositionMay 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: 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 1.2Jun 19, 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: Flagelliform spidroin variant 1
B: Flagelliform spidroin variant 1


Theoretical massNumber of molelcules
Total (without water)28,5132
Polymers28,5132
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-29 kcal/mol
Surface area10880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.878, 58.890, 46.330
Angle α, β, γ (deg.)90.000, 106.650, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Flagelliform spidroin variant 1


Mass: 14256.615 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nephila clavipes (spider) / Gene: Flag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S2B4P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: The crystals were obtained by siting drop vapor technique by mixing 1 ul of protein (10 mg/ml in 20 mM Na acetate, 10 mM NaCl, pH 5.5) with 1ul of 0.2M MgCl2, 0.1M bis-tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9788 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.8→44.39 Å / Num. obs: 18569 / % possible obs: 92.6 % / Redundancy: 5.4 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.103 / Rsym value: 0.094 / Net I/av σ(I): 4 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.93.60.3242688719060.1960.3810.3243.366
1.9-2.0140.2212.8931323110.1240.2550.2215.184.7
2.01-2.155.20.163.81306725100.0750.1780.16897.9
2.15-2.3260.1264.71475924510.0550.1380.12610.699.9
2.32-2.5560.1035.41339422170.0450.1130.10311.9100
2.55-2.856.20.0975.81247520140.0420.1070.09713.499.8
2.85-3.2960.0935.81079218100.0410.1020.09314.599.9
3.29-4.035.60.0865.8844715000.040.0950.08615.7100
4.03-5.696.20.0836.2735611840.0360.0910.08317.199.9
5.69-58.8960.0836.540006660.0370.0910.08316.499.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→44.39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.068 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 926 5 %RANDOM
Rwork0.186 ---
obs0.1876 17621 92.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.31 Å2 / Biso mean: 26.359 Å2 / Biso min: 10.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å2-0.37 Å2
2--2.25 Å20 Å2
3----1.05 Å2
Refinement stepCycle: final / Resolution: 1.8→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 0 71 1907
Biso mean---31.77 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131963
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181827
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.6212667
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5784220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5615268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27225.728103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46115342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.638157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022395
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02447
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 37 -
Rwork0.259 848 -
all-885 -
obs--59.72 %

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