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- PDB-9lie: Repetitive domain (RP) 2 structure of aciniform spidroin from Lat... -

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Basic information

Entry
Database: PDB / ID: 9lie
TitleRepetitive domain (RP) 2 structure of aciniform spidroin from Latrodectus hesperus
ComponentsAciniform spidroin 1
KeywordsSTRUCTURAL PROTEIN / Helix / spidroin / Repetitive domain
Function / homology
Function and homology information


Tubuliform egg casing silk strands structural domain / Tubuliform egg casing silk strands structural domain / Spidroin, C-terminal / Spidroin, repetitive domain / Major ampullate spidroin 1 and 2 / Spidroin, C-terminal domain superfamily / Spidroin, N-terminal / Major ampullate spidroin 1, spider silk protein 1, N-term / Spidroin, N-terminal domain superfamily / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain
Similarity search - Domain/homology
Aciniform spidroin 1
Similarity search - Component
Biological speciesLatrodectus hesperus (western black widow)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsYang, R. / Qin, R. / Yuan, W. / Lin, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The self-assemble of aciniform spidroin (AcSp) from Latrodectus hesperus
Authors: Yang, R. / Qin, R. / Yuan, W. / Lin, Z.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.875, 57.343, 66.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Aciniform spidroin 1


Mass: 15276.187 Da / Num. of mol.: 1 / Fragment: Repetitive domain (RP) 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Latrodectus hesperus (western black widow)
Gene: AcSp1 / Production host: Escherichia coli (E. coli) / References: UniProt: K7YP04
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris8.0 30% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.06→43.46 Å / Num. obs: 57444 / % possible obs: 95.9 % / Redundancy: 11.6 % / Biso Wilson estimate: 12.38 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.017 / Rrim(I) all: 0.059 / Net I/σ(I): 18.4
Reflection shellResolution: 1.06→1.11 Å / Num. unique obs: 7165 / CC1/2: 0.674 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.06→30.2 Å / SU ML: 0.1126 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.1469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2178 2803 4.92 %
Rwork0.2046 54216 -
obs0.2053 57019 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.06→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 216 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01291041
X-RAY DIFFRACTIONf_angle_d1.46661412
X-RAY DIFFRACTIONf_chiral_restr0.0901182
X-RAY DIFFRACTIONf_plane_restr0.0141180
X-RAY DIFFRACTIONf_dihedral_angle_d12.9858370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.080.311920.30681809X-RAY DIFFRACTION65.44
1.08-1.10.30761170.28832222X-RAY DIFFRACTION77.91
1.1-1.120.27491290.27752652X-RAY DIFFRACTION95.08
1.12-1.140.25191430.23732670X-RAY DIFFRACTION94.59
1.14-1.160.25861250.23292728X-RAY DIFFRACTION95.87
1.16-1.190.23671510.21872681X-RAY DIFFRACTION95.81
1.19-1.220.22371320.22082751X-RAY DIFFRACTION96.36
1.22-1.250.23151420.22092721X-RAY DIFFRACTION96.11
1.25-1.290.20711500.21862725X-RAY DIFFRACTION97.06
1.29-1.330.23981340.21832769X-RAY DIFFRACTION97.48
1.33-1.380.24511340.22982770X-RAY DIFFRACTION97.71
1.38-1.440.21091410.21742759X-RAY DIFFRACTION97.51
1.44-1.50.20781600.20052784X-RAY DIFFRACTION97.97
1.5-1.580.1971470.19492799X-RAY DIFFRACTION98.4
1.58-1.680.21461350.19642848X-RAY DIFFRACTION98.71
1.68-1.810.22971300.20672843X-RAY DIFFRACTION98.57
1.81-1.990.22551370.19712878X-RAY DIFFRACTION99.31
1.99-2.280.19841500.19092876X-RAY DIFFRACTION99.51
2.28-2.870.19611760.19092905X-RAY DIFFRACTION99.84
2.87-30.20.22511780.2033026X-RAY DIFFRACTION99.1

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