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- PDB-2lyn: HIGH RESOLUTION STRUCTURE OF RED ABALONE LYSIN DIMER -

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Basic information

Entry
Database: PDB / ID: 2lyn
TitleHIGH RESOLUTION STRUCTURE OF RED 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 rufescens (red abalone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsKresge, N. / Vacquier, V.D. / Stout, C.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: 1.35 and 2.07 A resolution structures of the red abalone sperm lysin monomer and dimer reveal features involved in receptor binding.
Authors: Kresge, N. / Vacquier, V.D. / Stout, C.D.
History
DepositionApr 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: SPERM LYSIN
D: SPERM LYSIN


Theoretical massNumber of molelcules
Total (without water)65,1814
Polymers65,1814
Non-polymers00
Water5,693316
1
A: SPERM LYSIN
B: SPERM LYSIN


Theoretical massNumber of molelcules
Total (without water)32,5902
Polymers32,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-16 kcal/mol
Surface area14400 Å2
MethodPISA
2
C: SPERM LYSIN
D: SPERM LYSIN


Theoretical massNumber of molelcules
Total (without water)32,5902
Polymers32,5902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-17 kcal/mol
Surface area14480 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-51 kcal/mol
Surface area25960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.520, 72.520, 266.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

21D-173-

HOH

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Components

#1: Protein
SPERM LYSIN


Mass: 16295.218 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Haliotis rufescens (red abalone) / Cell: SPERM / Organ: GONAD / Organelle: ACROSOME GRANULE / References: UniProt: P04552
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.69 Å3/Da / Density % sol: 53.88 %
Crystal growpH: 4.5
Details: 0.75 M (NH4)2SO4, 20 MM NH4SCN, 52.5 MM SODIUM-CITRATE-BORIC ACID BUFFER PH 4.5, 0.1 MM EDTA, 0.02% OTGP
Crystal grow
*PLUS
Temperature: 295 K / pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
250 mMsodium acetate1drop
30.1 %(w/v)1dropNaN3
40.75 Mammonium sulfate1reservoir
520 mM1reservoirNH4SCN
652.5 mMsodium citrate/boric acid/citric acid1reservoir
70.1 mMEDTA1reservoir
80.02 %1-S-octyl-beta-D-thioglucopyranoside1reservoir

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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: 2.07→40.5 Å / Num. obs: 44137 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rsym value: 0.087 / Net I/σ(I): 4.8
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.256 / % possible all: 94.6
Reflection
*PLUS
Redundancy: 6.9 % / Num. measured all: 948262 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 94.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.256

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Processing

Software
NameVersionClassification
AMoREphasing
SHELXLrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LYN

1lyn


Resolution: 2.07→100 Å / Num. parameters: 18473 / Num. restraintsaints: 17746 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2851 2197 5 %5% OF DATA
all0.2165 42965 --
obs0.213 -99.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4604
Refinement stepCycle: LAST / Resolution: 2.07→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 0 316 4618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.265
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.08
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
Lowest resolution: 40.5 Å / Rfactor Rfree: 0.285
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.55

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