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- PDB-1lis: THE CRYSTAL STRUCTURE OF A FERTILIZATION PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1lis
TitleTHE CRYSTAL STRUCTURE OF A FERTILIZATION PROTEIN
ComponentsLYSIN
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: 1.9 Å
AuthorsShaw, A. / Mcree, D.E. / Vacquier, V.D. / Stout, C.D.
CitationJournal: 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
DepositionJun 29, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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: LYSIN


Theoretical massNumber of molelcules
Total (without water)16,2951
Polymers16,2951
Non-polymers00
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.600, 45.900, 81.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LYSIN


Mass: 16295.218 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / References: UniProt: P04552
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion / PH range low: 7 / PH range high: 6.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
130.0-32.5 %sat1reservoiror 5%(w/v) PEG8000 (incubation at 29 C)(NH4)2SO4
250 mMBis-Tris-IDA1reservoiror 50 mM Bis-Tris-HCl
30.7 mMEDTA1reservoircan be done without EDTA
40.3 mMbenzamidine1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 15624 / Redundancy: 6.4 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.187 -
obs0.187 14806
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1097 0 0 84 1181
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.85
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
Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. reflection all: 14806 / Rfactor all: 0.187 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.9 Å2
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.85

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