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- PDB-5ii7: In-house sulfur-SAD structure of orthorhombic red abalone lysin a... -

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Basic information

Entry
Database: PDB / ID: 5ii7
TitleIn-house sulfur-SAD structure of orthorhombic red abalone lysin at 1.66 A resolution
ComponentsEgg-lysin
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / EGG-BINDING PROTEIN / ACROSOMAL PROTEIN / EGG COAT PENETRATION / CRYSTAL DEHYDRATION / SULFUR-SAD / S-SAD
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 / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSadat Al-Hosseini, H. / Raj, I. / Nishimura, K. / 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)17,54311
Polymers16,4831
Non-polymers1,06010
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-77 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.196, 51.195, 80.417
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
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.: 9 / 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.: 281 / 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: 56.6 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.66→43.186 Å / Num. obs: 34148 / % possible obs: 76 % / Redundancy: 4 % / Biso Wilson estimate: 13.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03454 / Net I/σ(I): 37.88
Reflection shellResolution: 1.662→1.721 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.1359 / Mean I/σ(I) obs: 6.41 / % possible all: 10

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Processing

Software
NameVersionClassification
PHENIX(dev_2386: ???)refinement
HKL-3000data reduction
PHASERphasing
Cootmodel building
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LIS

2lis


Resolution: 1.66→43.186 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3221 10.01 %Random selection
Rwork0.1562 ---
obs0.1594 32169 75.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→43.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 57 281 1456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061254
X-RAY DIFFRACTIONf_angle_d0.9651707
X-RAY DIFFRACTIONf_dihedral_angle_d12.48732
X-RAY DIFFRACTIONf_chiral_restr0.05169
X-RAY DIFFRACTIONf_plane_restr0.005206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6597-1.68450.4701100.258160X-RAY DIFFRACTION4
1.6845-1.71080.4228240.2347161X-RAY DIFFRACTION10
1.7108-1.73890.3041320.2335300X-RAY DIFFRACTION18
1.7389-1.76890.2346440.2251440X-RAY DIFFRACTION27
1.7689-1.8010.2675760.216612X-RAY DIFFRACTION37
1.801-1.83570.2114830.2126736X-RAY DIFFRACTION45
1.8357-1.87320.2206900.1919871X-RAY DIFFRACTION52
1.8732-1.91390.21311250.17141094X-RAY DIFFRACTION65
1.9139-1.95840.21941590.1771452X-RAY DIFFRACTION86
1.9584-2.00740.22571730.16231592X-RAY DIFFRACTION97
2.0074-2.06160.1851980.15631682X-RAY DIFFRACTION100
2.0616-2.12230.17891810.14621659X-RAY DIFFRACTION100
2.1223-2.19080.21121820.14451660X-RAY DIFFRACTION100
2.1908-2.26910.18291890.14181671X-RAY DIFFRACTION100
2.2691-2.360.1711860.1421658X-RAY DIFFRACTION100
2.36-2.46740.18521850.14811643X-RAY DIFFRACTION99
2.4674-2.59740.18491860.1531640X-RAY DIFFRACTION99
2.5974-2.76010.20171810.16181676X-RAY DIFFRACTION100
2.7601-2.97320.18841850.1721679X-RAY DIFFRACTION100
2.9732-3.27230.16461890.15441648X-RAY DIFFRACTION100
3.2723-3.74560.16571780.13811672X-RAY DIFFRACTION100
3.7456-4.71810.13481840.12851671X-RAY DIFFRACTION100
4.7181-43.20090.25351810.19061671X-RAY DIFFRACTION100

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