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- PDB-1fiz: THREE DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM BOAR SPERMATOZOA -

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Basic information

Entry
Database: PDB / ID: 1fiz
TitleTHREE DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM BOAR SPERMATOZOA
Components(BETA-ACROSIN ...) x 2
KeywordsHYDROLASE / anti-parallel beta-barrel
Function / homology
Function and homology information


acrosin / acrosomal matrix / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / serine-type endopeptidase activity ...acrosin / acrosomal matrix / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / serine-type endopeptidase activity / protein-containing complex / proteolysis
Similarity search - Function
Peptidase S1A, acrosin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin ...Peptidase S1A, acrosin / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
P-AMINO BENZAMIDINE / Acrosin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsTranter, R. / Read, J.A. / Jones, R. / Brady, R.L.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Effector sites in the three-dimensional structure of mammalian sperm beta-acrosin.
Authors: Tranter, R. / Read, J.A. / Jones, R. / Brady, R.L.
#1: Journal: Thesis
Title: Three dimensional structure of beta-acrosin from ram and boar spermatozoa
Authors: Tranter, R.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp ..._exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: BETA-ACROSIN HEAVY CHAIN
L: BETA-ACROSIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0998
Polymers31,8462
Non-polymers1,2536
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-48 kcal/mol
Surface area13980 Å2
MethodPISA
2
A: BETA-ACROSIN HEAVY CHAIN
L: BETA-ACROSIN LIGHT CHAIN
hetero molecules

A: BETA-ACROSIN HEAVY CHAIN
L: BETA-ACROSIN LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,19816
Polymers63,6924
Non-polymers2,50612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_656-z+5/4,-y+1/4,-x+5/41
Buried area7290 Å2
ΔGint-113 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.640, 130.640, 130.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Detailsheterodimer of chain A and B linked together by two disulphide bonds

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Components

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BETA-ACROSIN ... , 2 types, 2 molecules AL

#1: Protein BETA-ACROSIN HEAVY CHAIN


Mass: 29229.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: P08001
#2: Protein/peptide BETA-ACROSIN LIGHT CHAIN


Mass: 2615.991 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: P08001

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Sugars , 1 types, 1 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAca1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-2-3-4/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 30 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, ammonium sulphate, sodium cacodylate, p-aminobenzamidine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.375 mML-BAPNA1drop
20.1 MTris-HCl1drop
350 mM1dropCaCl2
50.1 Msodium cacodylate1reservoir
630 %PEG80001reservoir
70.2 Mammonium sulfate1reservoir
4protein1drop20mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.244
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 8303 / Num. obs: 8303 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 65.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.6
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.307 / Num. unique all: 1200 / % possible all: 99.8
Reflection
*PLUS
Num. obs: 8711

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.9→30 Å / SU B: 18.1713 / SU ML: 0.34735 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R Free: 0.41073
Details: maximun likelihood refinement CNS was also used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.26518 408 4.7 %RANDOM
Rwork0.21158 ---
all0.21409 8941 --
obs-8711 97.4 %-
Displacement parametersBiso mean: 47.027 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 79 25 2256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0290.021
X-RAY DIFFRACTIONp_angle_d2.651.986
X-RAY DIFFRACTIONp_angle_deg2.651.986
X-RAY DIFFRACTIONp_mcbond_it1.1881.5
X-RAY DIFFRACTIONp_mcangle_it2.2392
X-RAY DIFFRACTIONp_scbond_it3.4753
X-RAY DIFFRACTIONp_scangle_it5.6414.5
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1520.2
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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