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- PDB-1fiw: THREE-DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM RAM SPERMATOZOA -

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Basic information

Entry
Database: PDB / ID: 1fiw
TitleTHREE-DIMENSIONAL STRUCTURE OF BETA-ACROSIN FROM RAM SPERMATOZOA
Components
  • BETA-ACROSIN HEAVY CHAIN
  • BETA-ACROSIN LIGHT CHAIN
KeywordsHYDROLASE / anti-parallel beta-barrel
Function / homology
Function and homology information


acrosin / acrosome reaction / fucose binding / amidase activity / D-mannose binding / single fertilization / activation of adenylate cyclase activity / serine-type peptidase activity / acrosomal vesicle / serine-type endopeptidase activity / 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 speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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: To Be Published
Title: Three Dimensional Structure of 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: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms ...exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact
Item: _exptl_crystal_grow.temp / _pdbx_validate_close_contact.auth_atom_id_1 ..._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 / 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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 9, 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 / pdbx_unobs_or_zero_occ_residues
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)35,6105
Polymers34,4432
Non-polymers1,1673
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint14 kcal/mol
Surface area12870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.288, 105.288, 120.835
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsHeterodimer of chain A and L linked together by two disulphide bonds

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Components

#1: Protein BETA-ACROSIN HEAVY CHAIN


Mass: 32002.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: Q9GL10
#2: Protein/peptide BETA-ACROSIN LIGHT CHAIN


Mass: 2440.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Cell: SPERMATOZOA / Organ: TESTIS / References: UniProt: Q9GL10*PLUS
#3: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-L-Gulp]{}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PBZ / P-AMINO BENZAMIDINE


Mass: 136.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, sodium formate, p-aminobenzamidine, pH 4.6, 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 acetate1reservoir
62 Msodium formate1reservoir
4protein1drop12mg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 23810 / Num. obs: 20601 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 40.2 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.298 / Num. unique all: 2710 / % possible all: 92.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementResolution: 2.1→30 Å / SU B: 5.61319 / SU ML: 0.14893 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.20194 / ESU R Free: 0.18313 / Stereochemistry target values: Engh and Huber / Details: Maximum likelihood refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1120 5.2 %RANDOM
Rwork0.1974 ---
obs0.1996 20601 91.7 %-
all-23810 --
Displacement parametersBiso mean: 37.83 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å2-1 Å20 Å2
2---2 Å20 Å2
3---3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 80 191 2409
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.021
X-RAY DIFFRACTIONp_angle_d2.2421.968
X-RAY DIFFRACTIONp_chiral_restr0.1540.2
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_mcbond_it1.2761.5
X-RAY DIFFRACTIONp_mcangle_it2.192
X-RAY DIFFRACTIONp_scbond_it3.4243
X-RAY DIFFRACTIONp_scangle_it5.3884.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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