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- PDB-5ii8: Orthorhombic crystal structure of red abalone lysin at 0.99 A res... -

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Basic information

Entry
Database: PDB / ID: 5ii8
TitleOrthorhombic crystal structure of red abalone lysin at 0.99 A resolution
ComponentsEgg-lysin
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / EGG-BINDING PROTEIN / ACROSOMAL PROTEIN / EGG COAT PENETRATION / CRYSTAL DEHYDRATION
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: 0.99 Å
AuthorsSadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / De Sanctis, D. / Jovine, L.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Karolinska Institutet Sweden
Swedish Research Council2012-5093 Sweden
Goran Gustafsson Foundation for Research in Natural Sciences and Medicine Sweden
Sven and Ebba-Christina Hagberg foundation Sweden
European Molecular Biology Organization
European UnionERC 260759
Citation
Journal: Cell / Year: 2017
Title: Structural Basis of Egg Coat-Sperm Recognition at Fertilization.
Authors: Raj, I. / Sadat Al Hosseini, H. / Dioguardi, E. / Nishimura, K. / Han, L. / Villa, A. / de Sanctis, D. / Jovine, L.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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.
#2: 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.
#3: 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 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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

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Assembly

Deposited unit
A: Egg-lysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,92815
Polymers16,4831
Non-polymers1,44414
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-134 kcal/mol
Surface area8980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.210, 51.050, 80.530
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 Egg-lysin / Sperm-lysin


Mass: 16483.465 Da / Num. of mol.: 1 / Fragment: UNP residues 19-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / Plasmid: pJexpress411 / Details (production host): DNA2.0 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRARE star / References: UniProt: P04552
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.65 M ammonium sulfate, 0.2 M NaCl, 0.1 M CHES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.99→39.422 Å / Num. obs: 101171 / % possible obs: 94.12 % / Redundancy: 4.89 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 11.6
Reflection shellResolution: 0.99→1.01 Å / Redundancy: 4.86 % / Rmerge(I) obs: 2.006 / Mean I/σ(I) obs: 1.1 / % possible all: 87.44

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Processing

Software
NameVersionClassification
PHENIX(dev_2398: ???)refinement
XDS20141118data reduction
XDS20141118data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5II7

5ii7


Resolution: 0.99→39.422 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 9850 10.01 %Random selection
Rwork0.1642 ---
obs0.1669 98365 94.32 %-
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.99→39.422 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 77 224 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151245
X-RAY DIFFRACTIONf_angle_d1.3861693
X-RAY DIFFRACTIONf_dihedral_angle_d15.836464
X-RAY DIFFRACTIONf_chiral_restr0.096166
X-RAY DIFFRACTIONf_plane_restr0.01201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.99-1.00130.34993050.32082695X-RAY DIFFRACTION87
1.0013-1.0130.32022940.3072705X-RAY DIFFRACTION88
1.013-1.02540.32512990.2922753X-RAY DIFFRACTION88
1.0254-1.03840.30813020.28652659X-RAY DIFFRACTION87
1.0384-1.0520.30633150.26912806X-RAY DIFFRACTION90
1.052-1.06650.27773120.24582766X-RAY DIFFRACTION90
1.0665-1.08170.23773140.24512811X-RAY DIFFRACTION91
1.0817-1.09780.2283240.2262845X-RAY DIFFRACTION92
1.0978-1.1150.24743130.2112873X-RAY DIFFRACTION92
1.115-1.13330.21273240.19922897X-RAY DIFFRACTION93
1.1333-1.15280.21283190.17952896X-RAY DIFFRACTION94
1.1528-1.17380.19633140.1752860X-RAY DIFFRACTION92
1.1738-1.19640.20293240.17512949X-RAY DIFFRACTION95
1.1964-1.22080.20933330.16862957X-RAY DIFFRACTION95
1.2208-1.24730.1863290.16832962X-RAY DIFFRACTION95
1.2473-1.27630.20053330.15842955X-RAY DIFFRACTION95
1.2763-1.30830.18133300.15542979X-RAY DIFFRACTION96
1.3083-1.34360.16583390.14463018X-RAY DIFFRACTION97
1.3436-1.38320.17623330.14883016X-RAY DIFFRACTION97
1.3832-1.42780.1713230.14432957X-RAY DIFFRACTION95
1.4278-1.47890.14653370.13453043X-RAY DIFFRACTION97
1.4789-1.53810.17473420.1333049X-RAY DIFFRACTION97
1.5381-1.60810.16073390.13283058X-RAY DIFFRACTION98
1.6081-1.69290.15843400.13393073X-RAY DIFFRACTION98
1.6929-1.79890.17483470.13543101X-RAY DIFFRACTION98
1.7989-1.93780.14753430.14223074X-RAY DIFFRACTION98
1.9378-2.13280.15973430.14143114X-RAY DIFFRACTION98
2.1328-2.44140.16483530.153145X-RAY DIFFRACTION99
2.4414-3.07570.18613560.16863184X-RAY DIFFRACTION99
3.0757-39.45360.22093710.17663315X-RAY DIFFRACTION98

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