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- PDB-9lif: Repetitive domain (RP) 1 structure of aciniform spidroin from Lat... -

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Basic information

Entry
Database: PDB / ID: 9lif
TitleRepetitive domain (RP) 1 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: 1.38 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

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Assembly

Deposited unit
A: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)15,2331
Polymers15,2331
Non-polymers00
Water2,072115
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)25.439, 57.314, 35.000
Angle α, β, γ (deg.)90.000, 96.458, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Aciniform spidroin 1


Mass: 15233.163 Da / Num. of mol.: 1 / Fragment: Repetitive domain (RP) 1
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.: 115 / 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: 1.66 Å3/Da / Density % sol: 26.1 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris8.0 28% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.38→34.78 Å / Num. obs: 19796 / % possible obs: 96.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 14.93 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.6
Reflection shellResolution: 1.38→1.46 Å / Num. unique obs: 2782 / CC1/2: 0.865

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→29.73 Å / SU ML: 0.123 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.3113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1863 973 4.92 %
Rwork0.1571 18791 -
obs0.1585 19764 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.6 Å2
Refinement stepCycle: LAST / Resolution: 1.38→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1042 0 0 115 1157
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481049
X-RAY DIFFRACTIONf_angle_d0.65541425
X-RAY DIFFRACTIONf_chiral_restr0.0564184
X-RAY DIFFRACTIONf_plane_restr0.0047183
X-RAY DIFFRACTIONf_dihedral_angle_d11.5383372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.450.24281280.20152582X-RAY DIFFRACTION92.87
1.45-1.550.19391410.16812606X-RAY DIFFRACTION94.92
1.55-1.670.19371300.15052709X-RAY DIFFRACTION96.27
1.67-1.830.2021320.15212689X-RAY DIFFRACTION96.74
1.83-2.10.20391330.15032712X-RAY DIFFRACTION97.7
2.1-2.640.18371830.15272683X-RAY DIFFRACTION98.22
2.64-29.730.1711260.15842810X-RAY DIFFRACTION98.46

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