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- PDB-2lis: HIGH RESOLUTION STRUCTURE OF THE RED ABALONE LYSIN MONOMER -

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Basic information

Entry
Database: PDB / ID: 2lis
TitleHIGH RESOLUTION STRUCTURE OF THE RED ABALONE LYSIN MONOMER
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 / OTHER / Resolution: 1.35 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 16, 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 1.3Oct 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


Theoretical massNumber of molelcules
Total (without water)16,2951
Polymers16,2951
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.410, 45.310, 81.140
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 SPERM LYSIN


Mass: 16295.218 Da / Num. of mol.: 1 / 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.: 284 / 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: 2.9 Å3/Da / Density % sol: 57.3 %
Description: STRUCTURE WAS REFINED BY PHASE EXTENSION USING 1.9 A STRUCTURE OF RED ABALONE LYSIN MONOMER AS A STARTING POINT
Crystal growpH: 9.5
Details: 1.26 M AMMONIUM SULFATE, 100 MM CHESS PH 9.5, 200 MM NACL, pH 9.50
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: 1.35→18.6 Å / Num. obs: 41576 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rsym value: 4.5 / Net I/σ(I): 7.2
Reflection shellResolution: 1.35→1.38 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 8.6 / Rsym value: 8.2 / % possible all: 88.7
Reflection
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 18.6 Å / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Num. measured all: 259591 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.38 Å / % possible obs: 88.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 8.6

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Processing

Software
NameVersionClassification
SHELXLrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.35→100 Å / Num. parameters: 12587 / Num. restraintsaints: 14715 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.1787 2071 5 %5% OF
all0.1367 39350 --
obs0.1358 -97.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 1133 / Occupancy sum non hydrogen: 1388
Refinement stepCycle: LAST / Resolution: 1.35→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 284 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.272
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
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
Highest resolution: 1.35 Å / Lowest resolution: 100 Å / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.7 Å2

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