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- PDB-2w13: High-resolution crystal structure of the P-I snake venom metallop... -

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Basic information

Entry
Database: PDB / ID: 2w13
TitleHigh-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding
ComponentsZINC METALLOPROTEINASE BAP1
KeywordsHYDROLASE/INHIBITOR / HYDROLASE INHIBITOR COMPLEX / METZINCIN / CHEMOTAXIS / ADAMALYSINS / ENDOPEPTIDASE / METAL-BINDING / ZINC-DEPENDING / METALLOPROTEASE / METALLOPROTEINASE-INHIBITOR COMPLEX / ZINC / TOXIN / SECRETED / PROTEASE / HYDROLASE / P-I SNAKE VENOM METALLOPROTEINASE / ALPHA-BETA PROTEINS / MATRIXMETALLOPROTEINASE / TUMOR NECROSIS FACTOR ALPHA CONVERTING ENZYME / PYRROLIDONE CARBOXYLIC ACID / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / chemotaxis / toxin activity / proteolysis / extracellular region / metal ion binding
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
ACETATE ION / Chem-WR2 / Snake venom metalloproteinase BaP1
Similarity search - Component
Biological speciesBOTHROPS ASPER (terciopelo)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsLingott, T.J. / Schleberger, C. / Gutierrez, J.M. / Merfort, I.
Citation
Journal: Biochemistry / Year: 2009
Title: High-Resolution Crystal Structure of the Snake Venom Metalloproteinase Bap1 Complexed with a Peptidomimetic: Insight Into Inhibitor Binding.
Authors: Lingott, T.J. / Schleberger, C. / Gutierrez, J.M. / Merfort, I.
#1: 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.G. / Fox, J.W. / Gutierrez, J.M. / Arni, R.K.
History
DepositionOct 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZINC METALLOPROTEINASE BAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5947
Polymers22,7711
Non-polymers8236
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 59.600, 82.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ZINC METALLOPROTEINASE BAP1 / BAP1 / HEMORRHAGIC METALLOPROTEINASE BAP1 / BAP-1


Mass: 22770.740 Da / Num. of mol.: 1 / Fragment: RESIDUES 193-394 / Source method: isolated from a natural source / Source: (natural) BOTHROPS ASPER (terciopelo) / Secretion: VENOM
References: UniProt: P83512, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases

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Non-polymers , 5 types, 351 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-WR2 / (2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPYL)-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE


Mass: 455.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33N5O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.07 Å3/Da / Density % sol: 40.5 % / Description: NONE
Crystal growpH: 4.6 / Details: PEG 4000, NA(OAC), NH4(OAC), pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: KMC-1, DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. obs: 68715 / % possible obs: 98.7 % / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Biso Wilson estimate: 9.04 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.8
Reflection shellResolution: 1.14→1.21 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.4 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W12

2w12


Resolution: 1.14→18.15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.87 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMS OF LOOP 159-162 ARE MODELED (SEMI- OCCUPIED) IN TWO DIFFERENT CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16 2403 3.5 %RANDOM
Rwork0.13 ---
obs0.131 66242 100 %-
Displacement parametersBiso mean: 9.09 Å2
Refinement stepCycle: LAST / Resolution: 1.14→18.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 52 345 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211854
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.9582539
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16423.63688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27115312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7681513
X-RAY DIFFRACTIONr_chiral_restr0.1210.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021447
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.2895
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8091.51138
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.44221820
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2243794
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2764.5708
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.162 156
Rwork0.157 4317

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