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- PDB-1lyn: CRYSTAL STRUCTURE AND SUBUNIT DYNAMICS OF THE LYSIN DIMER: EGG EN... -

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Basic information

Entry
Database: PDB / ID: 1lyn
TitleCRYSTAL STRUCTURE AND SUBUNIT DYNAMICS OF THE LYSIN DIMER: EGG ENVELOPES DISSOCIATE DIMERS, THE MONOMER IS THE ACTIVE SPECIES
ComponentsSPERM LYSIN
KeywordsFERTILIZATION PROTEIN
Function / homology
Function and homology information


acrosomal lumen / single fertilization
Similarity search - Function
Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / Lysin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHaliotis rufescens (red abalone)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsShaw, A. / Vacquier, V.D. / Stout, C.D.
Citation
Journal: J.Cell Biol. / Year: 1995
Title: Crystal structure and subunit dynamics of the abalone sperm lysin dimer: egg envelopes dissociate dimers, the monomer is the active species.
Authors: Shaw, A. / Fortes, P.A. / Stout, C.D. / Vacquier, V.D.
#1: Journal: Science / Year: 1993
Title: The Crystal Structure of Lysin, a Fertilization Protein
Authors: Shaw, A. / Mcree, D.E. / Vacquier, V.D. / Stout, C.D.
History
DepositionMar 3, 1995Processing site: BNL
Revision 1.0Jun 3, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPERM LYSIN
B: SPERM LYSIN


Theoretical massNumber of molelcules
Total (without water)32,5902
Polymers32,5902
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.200, 47.000, 123.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein SPERM LYSIN


Mass: 16295.218 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / References: UniProt: P04552

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal grow
*PLUS
Method: vapor diffusion

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: 1993
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24754 / % possible obs: 93.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.054
Reflection
*PLUS
Highest resolution: 2.6 Å / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.8 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 11.3

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MARXDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.75→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.233 --
obs0.233 7328 93.6 %
Displacement parametersBiso mean: 13.2 Å2
Refinement stepCycle: LAST / Resolution: 2.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 0 0 2096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.05
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_plane_restr / Dev ideal: 1.73

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