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- PDB-5ii9: Monoclinic crystal structure of red abalone lysin at 2.11 A resolution -

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Basic information

Entry
Database: PDB / ID: 5ii9
TitleMonoclinic crystal structure of red abalone lysin at 2.11 A resolution
ComponentsEgg-lysin
KeywordsCELL ADHESION / FERTILIZATION / EGG-SPERM INTERACTION / GAMETE RECOGNITION / EGG-BINDING PROTEIN / ACROSOMAL PROTEIN / EGG COAT PENETRATION
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: 2.11 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: PDBE / 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

Downloads & links

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Assembly

Deposited unit
A: Egg-lysin
B: Egg-lysin
C: Egg-lysin
D: Egg-lysin
E: Egg-lysin
F: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)98,9016
Polymers98,9016
Non-polymers00
Water9,278515
1
A: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,4831
Polymers16,4831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.190, 69.340, 182.750
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Egg-lysin / Sperm-lysin


Mass: 16483.465 Da / Num. of mol.: 6
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 5% PEG 4000, 0.1 M sodium citrate, 0.2 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.028921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.028921 Å / Relative weight: 1
ReflectionResolution: 2.11→27.339 Å / Num. obs: 52122 / % possible obs: 92 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.47 Å2 / Rmerge(I) obs: 0.06107 / Net I/σ(I): 10.45
Reflection shellResolution: 2.11→2.19 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3794 / Mean I/σ(I) obs: 2.33 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
xia2data reduction
xia2data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LIS

2lis


Resolution: 2.11→27.34 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.93
RfactorNum. reflection% reflectionSelection details
Rfree0.229 2660 5.1 %Random selection
Rwork0.196 ---
obs0.198 52119 92 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.11→27.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 0 0 515 7119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046846
X-RAY DIFFRACTIONf_angle_d0.6159230
X-RAY DIFFRACTIONf_dihedral_angle_d9.2874122
X-RAY DIFFRACTIONf_chiral_restr0.043960
X-RAY DIFFRACTIONf_plane_restr0.0041148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1101-2.14840.28371390.26112557X-RAY DIFFRACTION89
2.1484-2.18970.31420.25032468X-RAY DIFFRACTION88
2.1897-2.23440.25891390.24242568X-RAY DIFFRACTION93
2.2344-2.2830.29721350.24622665X-RAY DIFFRACTION94
2.283-2.3360.23471540.23182635X-RAY DIFFRACTION95
2.336-2.39440.30111430.23472661X-RAY DIFFRACTION95
2.3944-2.45910.29051340.22082685X-RAY DIFFRACTION94
2.4591-2.53140.24521520.2332574X-RAY DIFFRACTION93
2.5314-2.61310.2581430.22312596X-RAY DIFFRACTION90
2.6131-2.70640.27361450.2152493X-RAY DIFFRACTION92
2.7064-2.81460.24041530.22142730X-RAY DIFFRACTION95
2.8146-2.94260.25781290.2132656X-RAY DIFFRACTION95
2.9426-3.09750.21821220.20852660X-RAY DIFFRACTION94
3.0975-3.29130.2281280.19622631X-RAY DIFFRACTION92
3.2913-3.54490.2351090.19422502X-RAY DIFFRACTION88
3.5449-3.90080.19931410.16812681X-RAY DIFFRACTION93
3.9008-4.46310.20151640.15062569X-RAY DIFFRACTION92
4.4631-5.6150.18031450.15342527X-RAY DIFFRACTION89
5.615-27.34090.19021430.17532601X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.00010.00010.00140.00190.00030.0013-0.0159-0.013-0.0057-0.0161-0.00330.0111-0.00060.01-00.19660.0479-0.00970.173-0.00710.24627.611836.2417.4845
2-0.0026-0.0024-0.01640.00640.00010.0055-0.02920.0080.036-0.0236-0.1251-0.06430.0625-0.0602-00.0885-0.01070.03250.06550.08730.13198.843855.93313.6267
30.00120.00070.00080.0012-0.00010.00170.00670.0088-0.00320.0086-0.00570.0012-0.009-0.0018-00.3001-0.0357-0.00010.2882-0.04120.292-8.323915.200772.9645
40.0063-0.00320.00860.00740.00730.0104-0.0073-0.0570.0391-0.02740.00240.03570.084-0.017100.1436-0.00630.02610.1582-0.02580.1331-9.044333.551488.5651
50.00030.0011-0.00010.00240.00020.001-0.0089-0.0028-0.00010.0054-0.0033-0.00020.0015-0.002300.2512-0.0041-0.04850.2866-0.02810.1904-6.770953.66135.6297
60.0140.0009-0.00390.00490.004-0.0001-0.1252-0.0186-0.06170.0156-0.0414-0.0528-0.0629-0.002100.11660.05890.08850.13650.00590.1169-4.668833.136225.3601
70.0008-0.00050.00020.00010.00010.0002-0.0029-0.0017-0.0028-0.00450.0037-0.0006-0.00580.003100.23540.02290.02230.2964-0.03180.285618.956440.457481.4122
80-0.0003-0.00020.00020.00050.00050.00110.002-0.0030.0105-0.0081-0.0036-0.00420.004-00.2853-0.0432-0.04510.32280.06030.331220.603561.525410.6429
9-0.0056-0.00130.01130.00350.00770.0018-0.157-0.11660.1245-0.0980.04060.0090.0310.06270-0.0248-0.1407-0.38420.0904-0.1743-0.028621.19863.517734.5276
10-0.0002-0.0004-0.00110.00070.00010.00010.01210.0024-0.0003-0.00150.01180.00030.0116-0.002900.2618-0.03380.01380.34360.08310.27114.6523104.846656.9526
110.00660.00230.00120.0056-0.00480.0091-0.05220.0456-0.0784-0.00610.0096-0.0023-0.00140.0161-00.1597-0.05290.02290.1666-0.04510.17833.678982.14564.3924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESI 22:30
2X-RAY DIFFRACTION2CHAIN A AND RESI 31:152
3X-RAY DIFFRACTION3CHAIN B AND RESI 22:30
4X-RAY DIFFRACTION4CHAIN B AND RESI 31:152
5X-RAY DIFFRACTION5CHAIN C AND RESI 23:30
6X-RAY DIFFRACTION6CHAIN C AND RESI 31:152
7X-RAY DIFFRACTION7CHAIN D AND RESI 23:30
8X-RAY DIFFRACTION8CHAIN E AND RESI 22:30
9X-RAY DIFFRACTION9CHAIN E AND RESI 31:152
10X-RAY DIFFRACTION10CHAIN F AND RESI 22:30
11X-RAY DIFFRACTION11CHAIN F AND RESI 31:152

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