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- PDB-9lki: N-terminal domain (NTD) structure of aciniform spidroin 1(AcSp1) ... -

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Basic information

Entry
Database: PDB / ID: 9lki
TitleN-terminal domain (NTD) structure of aciniform spidroin 1(AcSp1) from Latrodectus hesperus
ComponentsAciniform spidroin 1
KeywordsSTRUCTURAL PROTEIN / Helix / spidroin / N-terminal
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: 2.98 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 N-terminal domain of aciniform spidroin 1 (AcSp1) from Latrodectus hesperus
Authors: Yang, R. / Qin, R. / Yuan, W. / Lin, Z.
History
DepositionJan 16, 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
D: Aciniform spidroin 1
C: Aciniform spidroin 1
A: Aciniform spidroin 1
B: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)62,2864
Polymers62,2864
Non-polymers00
Water19811
1
D: Aciniform spidroin 1
C: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)31,1432
Polymers31,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-26 kcal/mol
Surface area10670 Å2
MethodPISA
2
A: Aciniform spidroin 1
B: Aciniform spidroin 1


Theoretical massNumber of molelcules
Total (without water)31,1432
Polymers31,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-23 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.620, 82.340, 65.440
Angle α, β, γ (deg.)90.000, 94.163, 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: 15571.514 Da / Num. of mol.: 4 / Fragment: N-terminal domain
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.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.77 Å3/Da / Density % sol: 30.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 10% v/v 2-Propanol 0.1 M Sodium acetate trihydrate pH 4.0 22% w/v Polyethylene glycol 6,000

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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: Dec 1, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.98→41.17 Å / Num. obs: 8805 / % possible obs: 99.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 75.26 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.376 / Rpim(I) all: 0.167 / Rrim(I) all: 0.413 / Net I/σ(I): 5.5
Reflection shellResolution: 2.98→3.06 Å / Rmerge(I) obs: 2.175 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 650 / Rpim(I) all: 0.885 / Rrim(I) all: 2.351

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→40.51 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.322 449 5.11 %
Rwork0.289 8339 -
obs0.2912 8788 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.26 Å2
Refinement stepCycle: LAST / Resolution: 2.98→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 0 11 3775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493820
X-RAY DIFFRACTIONf_angle_d0.75945131
X-RAY DIFFRACTIONf_chiral_restr0.0432584
X-RAY DIFFRACTIONf_plane_restr0.0047663
X-RAY DIFFRACTIONf_dihedral_angle_d15.82441429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.410.34921130.3592810X-RAY DIFFRACTION99.42
3.41-4.30.39351690.31942727X-RAY DIFFRACTION98.77
4.3-40.510.27821670.25142802X-RAY DIFFRACTION98.93

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