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- PDB-4yf2: Crystal structure of mouse sperm C-type lysozyme-like protein 1 -

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Basic information

Entry
Database: PDB / ID: 4yf2
TitleCrystal structure of mouse sperm C-type lysozyme-like protein 1
ComponentsSperm acrosome membrane-associated protein 3
KeywordsCELL ADHESION / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


acrosomal matrix / sperm-egg recognition / fusion of sperm to egg plasma membrane involved in single fertilization / acrosomal membrane / acrosomal vesicle / secretory granule / lysozyme activity / defense response to Gram-negative bacterium / membrane => GO:0016020 / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Lysozyme-like protein 3 / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme ...Lysozyme-like protein 3 / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Sperm acrosome membrane-associated protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsZheng, H. / Mandal, A. / Shumilin, I.A. / Shabalin, I.G. / Herr, J.C. / Minor, W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM53163 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM62414 United States
CitationJournal: Andrology / Year: 2015
Title: Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.
Authors: Zheng, H. / Mandal, A. / Shumilin, I.A. / Chordia, M.D. / Panneerdoss, S. / Herr, J.C. / Minor, W.
History
DepositionFeb 24, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMar 11, 2015ID: 2GOI
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sperm acrosome membrane-associated protein 3
B: Sperm acrosome membrane-associated protein 3
C: Sperm acrosome membrane-associated protein 3


Theoretical massNumber of molelcules
Total (without water)47,7023
Polymers47,7023
Non-polymers00
Water2,378132
1
A: Sperm acrosome membrane-associated protein 3


Theoretical massNumber of molelcules
Total (without water)15,9011
Polymers15,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sperm acrosome membrane-associated protein 3


Theoretical massNumber of molelcules
Total (without water)15,9011
Polymers15,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sperm acrosome membrane-associated protein 3


Theoretical massNumber of molelcules
Total (without water)15,9011
Polymers15,9011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.592, 136.592, 33.315
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA0 - 1272 - 129
21ASPASPBB0 - 1272 - 129
12GLYGLYAA0 - 1252 - 127
22GLYGLYCC0 - 1252 - 127
13GLYGLYBB0 - 1252 - 127
23GLYGLYCC0 - 1252 - 127

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Sperm acrosome membrane-associated protein 3 / Lysozyme-like protein 3 / Sperm lysozyme-like protein 1 / mSLLP1


Mass: 15900.758 Da / Num. of mol.: 3 / Fragment: UNP residues 93-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Spaca3, Lyc3, Lyzl3, Sllp1 / Plasmid: pET28b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9D9X8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris, 20% w/v PEG5000 MME, 20% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. all: 19824 / Num. obs: 19790 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.918 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LSG

1lsg


Resolution: 2.15→50.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 13.557 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21747 1030 5.2 %RANDOM
Rwork0.18821 ---
obs0.18978 18760 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 0 132 3178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193135
X-RAY DIFFRACTIONr_bond_other_d0.0070.022777
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9114260
X-RAY DIFFRACTIONr_angle_other_deg1.23836341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2745383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59423.602161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0351522
X-RAY DIFFRACTIONr_chiral_restr0.1080.2438
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023653
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02817
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9032.7621541
X-RAY DIFFRACTIONr_mcbond_other1.9042.7611540
X-RAY DIFFRACTIONr_mcangle_it3.2274.1341921
X-RAY DIFFRACTIONr_mcangle_other3.2264.1351922
X-RAY DIFFRACTIONr_scbond_it2.1652.921594
X-RAY DIFFRACTIONr_scbond_other2.1652.921594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4784.3022340
X-RAY DIFFRACTIONr_long_range_B_refined6.11622.3123757
X-RAY DIFFRACTIONr_long_range_B_other6.11322.33755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A144900.03
12B144900.03
21A143080.03
22C143080.03
31B143300.04
32C143300.04
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 56 -
Rwork0.255 1395 -
obs--99.45 %
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)
14.50470.42620.51612.84011.23752.55930.0480.058-0.4245-0.04860.0073-0.06550.11830.0871-0.05540.06450.0130.02490.0244-0.01840.0699-0.907-25.534-5.974
21.5667-0.5673-0.21373.29891.41244.4376-0.0784-0.01840.0084-0.08570.05820.0195-0.0801-0.23290.02020.10220.0085-0.02850.0271-0.0190.0417-6.707-54.2795.268
36.30371.63830.43284.09110.50294.11470.1717-0.36040.399-0.0055-0.17970.35110.0411-0.56860.0080.0894-0.04520.04270.1055-0.03610.0576-24.548-72.307-0.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 129
2X-RAY DIFFRACTION2B0 - 128
3X-RAY DIFFRACTION3C0 - 126

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