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- PDB-7wns: Crystal structure of ENF peptide binding protein from Silkworm -

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Basic information

Entry
Database: PDB / ID: 7wns
TitleCrystal structure of ENF peptide binding protein from Silkworm
Components30K protein 12
KeywordsPEPTIDE BINDING PROTEIN / paralytic peptide / imunity
Function / homologyLepidopteran low molecular weight lipoprotein / Lepidopteran low molecular weight lipoprotein, N-terminal domain / Lepidopteran low molecular weight (30 kD) lipoprotein / extracellular region / 30K protein 12
Function and homology information
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.799 Å
AuthorsGuo, P.C. / Zhang, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
National Natural Science Foundation of China (NSFC)32030103 China
CitationJournal: To Be Published
Title: Crysatl structure of ENF-peptide binding protein from silkworm, Bombyx mori.
Authors: Guo, P.C. / Zhang, H.
History
DepositionJan 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 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: 30K protein 12


Theoretical massNumber of molelcules
Total (without water)50,8461
Polymers50,8461
Non-polymers00
Water8,215456
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)54.477, 121.692, 253.769
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein 30K protein 12


Mass: 50846.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: 101739532 / Production host: Escherichia coli (E. coli) / References: UniProt: H9B445
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 4.22 Å3/Da / Density % sol: 70.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: O.5M magnesium formate, 0.1M Bis-Tris pH 6.5 / PH range: 6.5-7.5 / Temp details: 16

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 78393 / % possible obs: 99.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 36.67
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 3 / Num. unique obs: 3823 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.799→35.543 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1853 3936 5.035 %RANDOM
Rwork0.1733 74242 --
all0.174 ---
obs-78178 99.279 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.324 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20 Å20 Å2
2---0.106 Å2-0 Å2
3---0.103 Å2
Refinement stepCycle: LAST / Resolution: 1.799→35.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 456 3890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133533
X-RAY DIFFRACTIONr_bond_other_d0.0350.0173211
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.6384802
X-RAY DIFFRACTIONr_angle_other_deg2.411.5897385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3665427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14823.029208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47415584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2231521
X-RAY DIFFRACTIONr_chiral_restr0.1090.2436
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024090
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02864
X-RAY DIFFRACTIONr_nbd_refined0.2080.2692
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.23137
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21756
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2349
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.28
X-RAY DIFFRACTIONr_nbd_other0.2250.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1730.217
X-RAY DIFFRACTIONr_mcbond_it3.6792.7241702
X-RAY DIFFRACTIONr_mcbond_other3.6722.7231701
X-RAY DIFFRACTIONr_mcangle_it4.844.0642128
X-RAY DIFFRACTIONr_mcangle_other4.844.0642129
X-RAY DIFFRACTIONr_scbond_it4.2443.1061830
X-RAY DIFFRACTIONr_scbond_other4.2433.1071831
X-RAY DIFFRACTIONr_scangle_it6.4054.5072673
X-RAY DIFFRACTIONr_scangle_other6.4044.5082674
X-RAY DIFFRACTIONr_lrange_it8.4433.3324251
X-RAY DIFFRACTIONr_lrange_other8.26532.6074124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.8460.2512850.2415246X-RAY DIFFRACTION95.8413
1.846-1.8960.2192920.2145231X-RAY DIFFRACTION98.9253
1.896-1.9510.2212900.2095126X-RAY DIFFRACTION99.1397
1.951-2.0110.1992640.1875029X-RAY DIFFRACTION99.25
2.011-2.0770.1932520.1854864X-RAY DIFFRACTION99.3398
2.077-2.150.1922230.1744725X-RAY DIFFRACTION99.3973
2.15-2.2310.1872370.1714541X-RAY DIFFRACTION99.5002
2.231-2.3220.1722150.1694405X-RAY DIFFRACTION99.5475
2.322-2.4260.1742250.1754213X-RAY DIFFRACTION99.6184
2.426-2.5440.1722000.1614070X-RAY DIFFRACTION99.6965
2.544-2.6820.1752330.1673831X-RAY DIFFRACTION99.828
2.682-2.8440.1931880.1733631X-RAY DIFFRACTION99.8692
2.844-3.0410.1841960.1743459X-RAY DIFFRACTION99.918
3.041-3.2840.1781740.1693193X-RAY DIFFRACTION99.911
3.284-3.5980.1751500.1672973X-RAY DIFFRACTION100
3.598-4.0220.1741590.1622681X-RAY DIFFRACTION99.9648
4.022-4.6440.1711140.1352422X-RAY DIFFRACTION100
4.644-5.6880.1561080.1642050X-RAY DIFFRACTION100
5.688-8.0420.222750.2011618X-RAY DIFFRACTION99.941
8.042-35.5430.204560.18931X-RAY DIFFRACTION98.503

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