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- PDB-1iag: FIRST STRUCTURE OF A SNAKE VENOM METALLOPROTEINASE: A PROTOTYPE F... -

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Basic information

Entry
Database: PDB / ID: 1iag
TitleFIRST STRUCTURE OF A SNAKE VENOM METALLOPROTEINASE: A PROTOTYPE FOR MATRIX METALLOPROTEINASES(SLASH)COLLAGENASES
ComponentsADAMALYSIN II
KeywordsMETALLOPROTEASE
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
Snake venom metalloproteinase adamalysin-2
Similarity search - Component
Biological speciesCrotalus adamanteus (eastern diamondback rattlesnake)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsGomis-Rueth, F.-X. / Bode, W.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Refined 2.0 Angstroms X-Ray Crystal Structure of the Snake Venom Zinc-Endopeptidase Adamalysin II. Primary and Tertiary Structure Determination, Refinement, Molecular Structure and Comparison ...Title: Refined 2.0 Angstroms 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-Rueth, F.X. / Kress, L.F. / Kellermann, J. / Mayr, I. / Lee, X. / Huber, R. / Bode, W.
#2: Journal: Embo J. / Year: 1994
Title: The X-Ray Crystal Structure of the Catalytic Domain of Human Neutrophil Collagenase Inhibited by a Substrate Analogue Reveals the Essentials for Catalysis and Specificity
Authors: Bode, W. / Reinemer, P. / Huber, R. / Kleine, T. / Schnierer, S. / Tschesche, H.
#3: Journal: FEBS Lett. / Year: 1994
Title: Structural Implications for the Role of the N Terminus in the 'Superactivation' of Collagenases. A Crystallographic Study
Authors: Reinemer, P. / Grams, F. / Huber, R. / Kleine, T. / Schnierer, S. / Piper, M. / Tschesche, H. / Bode, W.
#4: Journal: FEBS Lett. / Year: 1993
Title: Astacins, Serralysins, Snake Venom and Matrix Metalloproteinases Exhibit Identical Zinc-Binding Environments (Hexxhxxgxxh and met-Turn) and Topologies and Should be Grouped Into a Common Family, the 'Metzincins'
Authors: Bode, W. / Gomis-Rueth, F.-X. / Stoecker, W.
#5: Journal: Nature / Year: 1992
Title: Structure of Astacin and Implications for Activation of Astacins and Zinc-Ligation of Collagenases
Authors: Bode, W. / Gomis-Rueth, F.X. / Huber, R. / Zwilling, R. / Stoecker, W.
History
DepositionMay 9, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: 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)23,4134
Polymers23,2121
Non-polymers2023
Water3,117173
1
A: ADAMALYSIN II
hetero molecules

A: ADAMALYSIN II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8268
Polymers46,4232
Non-polymers4036
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556x,x-y,-z+11
Unit cell
Length a, b, c (Å)73.600, 73.600, 96.400
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: 23211.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crotalus adamanteus (eastern diamondback rattlesnake)
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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

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Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal grow
*PLUS
pH: 5 / Method: unknown
Components of the solutions
*PLUS
Conc.: 1.8 M / Common name: ammonium sulfate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 17021 / % possible obs: 83 % / Num. measured all: 24244 / Rmerge(I) obs: 0.0544
Reflection shell
*PLUS
Highest resolution: 2.03 Å / Lowest resolution: 2.09 Å / % possible obs: 42 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→8 Å / Rfactor Rwork: 0.172 / Rfactor obs: 0.172
Details: 158 OF THE 203 RESIDUES HAVE BEEN CHECKED BY PEPTIDE SEQUENCING. THE REMAINING 45 AMINO ACID RESIDUES HAVE BEEN IDENTIFIED ONLY FROM THEIR DENSITY (FOR DISCUSSION, SEE GOMIS-RUETH ET AL. ...Details: 158 OF THE 203 RESIDUES HAVE BEEN CHECKED BY PEPTIDE SEQUENCING. THE REMAINING 45 AMINO ACID RESIDUES HAVE BEEN IDENTIFIED ONLY FROM THEIR DENSITY (FOR DISCUSSION, SEE GOMIS-RUETH ET AL. (1994) J.MOL.BIOL, 239, 513-544, AND FIGURES 1 AND 2.
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 7 173 1800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 16776 / Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.9

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