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- PDB-1nd1: Amino acid sequence and crystal structure of BaP1, a metalloprote... -

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Basic information

Entry
Database: PDB / ID: 1nd1
TitleAmino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities.
ComponentsBaP1
KeywordsTOXIN / metalloproteinase / snake venom / three-disulfide
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / chemotaxis / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. ...Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Snake venom metalloproteinase BaP1
Similarity search - Component
Biological speciesBothrops asper (terciopelo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWatanabe, L. / Shannon, J.D. / Valente, R.H. / Rucavado, A. / Alape-Giron, A. / Kamiguti, A.S. / Theakston, R.D. / Fox, J.W. / Gutierrez, J.M. / Arni, R.K.
Citation
Journal: Protein Sci. / Year: 2003
Title: Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities
Authors: Watanabe, L. / Shannon, J.D. / Valente, R.H. / Rucavado, A. / Alape-Giron, A. / Kamiguti, A.S. / Theakston, R.D. / Fox, J.W. / Gutierrez, J.M. / Arni, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases.
Authors: Zhu, X. / Teng, M. / Niu, L.
#2: Journal: J.Mol.Biol. / Year: 1998
Title: Crystal Structures of Acutolysin A, a three-disulfide hemorrhagic zinc metalloproteinase from the snake venom of Agkistrodon acutus.
Authors: Gong, W. / Zhu, X. / Liu, S. / Teng, M. / Niu, L.
History
DepositionDec 6, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BaP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8132
Polymers22,7481
Non-polymers651
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.425, 60.364, 86.257
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 BaP1


Mass: 22747.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bothrops asper (terciopelo) / Secretion: Venom / References: UniProt: P83512
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.09 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 20000, dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG200001reservoirpH9.0
32 %(v/v)dioxane1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 23, 2002
RadiationMonochromator: Graphite / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→500 Å / Num. all: 14941 / Num. obs: 49843 / % possible obs: 92.1 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.072
Reflection shellResolution: 1.9→1.97 Å / Num. unique all: 816 / Rsym value: 0.28 / % possible all: 51.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 14941 / Num. measured all: 49843 / Rmerge(I) obs: 0.072

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB_ID 1QUA

1qua


Resolution: 1.93→18.31 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1182665.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 742 5 %RANDOM
Rwork0.191 ---
obs0.191 14169 95.2 %-
all-14911 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.7738 Å2 / ksol: 0.306696 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.8 Å20 Å20 Å2
2--1.08 Å20 Å2
3---1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.93→18.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 1 110 1707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.642
X-RAY DIFFRACTIONc_scbond_it3.132
X-RAY DIFFRACTIONc_scangle_it4.652.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 81 5.1 %
Rwork0.282 1506 -
obs--59.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP1.PARAMPROTEIN1.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2159 / Rfactor Rwork: 0.1908
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.00995
X-RAY DIFFRACTIONc_angle_deg2.2566
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.21

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