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- PDB-4aig: ADAMALYSIN II WITH PHOSPHONATE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 4aig
TitleADAMALYSIN II WITH PHOSPHONATE INHIBITOR
ComponentsADAMALYSIN II
KeywordsMETALLOENDOPEPTIDASE / SNAKE VENOM METALLOENDOPEPTIDASE / ZINC PROTEASE
Function / homology
Function and homology information


adamalysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
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
Chem-FLX / Snake venom metalloproteinase adamalysin-2
Similarity search - Component
Biological speciesCrotalus adamanteus (eastern diamondback rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPochetti, G. / Mazza, F. / Gavuzzo, E. / Cirilli, M.
Citation
Journal: FEBS Lett. / Year: 1997
Title: 2 angstrom X-ray structure of adamalysin II complexed with a peptide phosphonate inhibitor adopting a retro-binding mode.
Authors: Cirilli, M. / Gallina, C. / Gavuzzo, E. / Giordano, C. / Gomis-Ruth, F.X. / Gorini, B. / Kress, L.F. / Mazza, F. / Paradisi, M.P. / Pochetti, G. / Politi, V.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with ...Title: Refined 2.0 A X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison with Astacin, Collagenase and Thermolysin
Authors: Gomis-Ruth, F.X. / Kress, L.F. / Kellermann, J. / Mayr, I. / Lee, X. / Huber, R. / Bode, W.
#2: Journal: Embo J. / Year: 1993
Title: First Structure of a Snake Venom Metalloproteinase: A Prototype for Matrix Metalloproteinases/Collagenases
Authors: Gomis-Ruth, F.X. / Kress, L.F. / Bode, W.
History
DepositionOct 16, 1997Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5944
Polymers23,0411
Non-polymers5533
Water3,441191
1
A: ADAMALYSIN II
hetero molecules

A: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1898
Polymers46,0832
Non-polymers1,1066
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
Unit cell
Length a, b, c (Å)73.500, 73.500, 96.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein ADAMALYSIN II


Mass: 23041.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Crotalus adamanteus (eastern diamondback rattlesnake)
Secretion: VENOM / References: UniProt: P34179, adamalysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FLX / N-[(FURAN-2-YL)CARBONYL]-(S)-LEUCYL-(R)-[1-AMINO-2(1H-INDOL-3-YL)ETHYL]-PHOSPHONIC ACID


Mass: 447.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N3O6P
#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: 4

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growDetails: 1.8 M AMMONIUM SULPHATE
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
24 mM1dropCaCl2
34 mM1dropZnCl2
40.8 mg/mlinhibitor1drop
58 mMTris1drop
60.36 Mammonium sulfate1drop
71.8 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 19533 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 4
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 53112
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAG

1iag


Resolution: 2→6 Å / σ(F): 2
Details: RESIDUE ASN 2 WAS NOT REFINED (FOCC=0) DUE TO NO CLEAR DENSITY.
RfactorNum. reflection
Rwork0.177 -
obs0.177 18583
Displacement parametersBiso mean: 17.3 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 0 33 191 1831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.95
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 17.307 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54

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