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- PDB-3lyn: STRUCTURE OF GREEN ABALONE LYSIN DIMER -

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Basic information

Entry
Database: PDB / ID: 3lyn
TitleSTRUCTURE OF GREEN ABALONE LYSIN DIMER
ComponentsSPERM LYSIN
KeywordsCELL ADHESION / ABALONE LYSIN / FERTILIZATION PROTEIN / GAMETE RECOGNITION 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 fulgens (green abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsKresge, N. / Vacquier, V.D. / Stout, C.D.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The high resolution crystal structure of green abalone sperm lysin: implications for species-specific binding of the egg receptor.
Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D.
History
DepositionMay 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,6922
Polymers32,6922
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.170, 119.170, 51.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein SPERM LYSIN


Mass: 16346.247 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Haliotis fulgens (green abalone) / Cell: SPERM / Organ: GONAD / Organelle: ACROSOME GRANULE / References: UniProt: Q01381
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 3.28 Å3/Da / Density % sol: 63.2 %
Crystal growpH: 4
Details: 1.26 M AMMONIUM SULFATE 0.10 M SODIUM ACETATE 0.20 M SODIUM CHLORIDE, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.71→25.7 Å / Num. obs: 44479 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rsym value: 5.1 / Net I/σ(I): 9.7
Reflection shellResolution: 1.71→1.75 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.9 / Rsym value: 38.7 / % possible all: 92.1
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 92.1 % / Rmerge(I) obs: 0.387

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
SHELXLrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→100 Å / Num. parameters: 9088 / Num. restraintsaints: 8445 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: TER LYS: C-TERMINAL RESIDUES OF CHAIN A ASN 133, HIS 134, GLY 135 AND LYS 136 WERE NOT SEEN IN DENSITY HIS: C-TERMINAL RESIDUES OF CHAIN B GLY 135 AND LYS 136 WERE NOT SEEN IN DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 2588 5 %5% OF DATA
all0.2148 44062 --
obs0.2129 -97.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2268
Refinement stepCycle: LAST / Resolution: 1.7→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 0 218 2271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.26
X-RAY DIFFRACTIONs_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.215 / Rfactor Rfree: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.89

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