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- PDB-1gbk: ALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH ME... -

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Basic information

Entry
Database: PDB / ID: 1gbk
TitleALPHA-LYTIC PROTEASE WITH MET 190 REPLACED BY ALA COMPLEX WITH METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID
Components
  • ALPHA-LYTIC PROTEASE
  • METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID INHIBITOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ACTIVE-SITE MUTATION / SERINE PROTEINASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / 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
METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.13 Å
AuthorsMace, J.E. / Agard, D.A.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Kinetic and structural characterization of mutations of glycine 216 in alpha-lytic protease: a new target for engineering substrate specificity.
Authors: Mace, J.E. / Agard, D.A.
#1: Journal: Biochemistry / Year: 1991
Title: Structural Basis for Broad Specificity in Alpha-Lytic Protease
Authors: Bone, R. / Fujushige, A. / Kettner, C.A. / Agard, D.A.
#2: Journal: Nature / Year: 1989
Title: Structural Plasticity Broadens the Specificity of an Engineered Protease
Authors: Bone, R. / Silen, J.L. / Agard, D.A.
#3: Journal: Biochemistry / Year: 1989
Title: Structural Analysis of Specificity: Alpha-Lytic Protease Complexes with Analogues of Reaction Intermediates
Authors: Bone, R. / Frank, D. / Kettner, D. / Agard, D.A.
#4: Journal: Biochemistry / Year: 1987
Title: Serine Protease Mechanism: Structure of an Inhibitory Complex of Alpha-Lytic Protease and a Tightly Bound Peptide Boronic Acid
Authors: Bone, R. / Shenvi, A.B. / Kettner, C.A. / Agard, D.A.
#5: Journal: J.Mol.Biol. / Year: 1985
Title: Refined Structure of Alpha-Lytic Protease at 1.7 Angstroms Resolution. Analysis of Hydrogen Bonding and Solvent Structure
Authors: Fujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#6: Journal: J.Mol.Biol. / Year: 1979
Title: Molecular Structure of the Alpha-Lytic Protease from Myxobacter 495 at 2.8 Angstroms Resolution
Authors: Brayer, G.D. / Delbaere, L.T.J. / James, M.N.G.
History
DepositionSep 6, 1995Processing site: BNL
SupersessionJan 29, 1996ID: 1LPR
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Jun 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 / struct_conn / struct_ref_seq / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-LYTIC PROTEASE
P: METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4494
Polymers20,2572
Non-polymers1922
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-21 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.360, 66.360, 80.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 19815.014 Da / Num. of mol.: 1 / Mutation: M190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Strain: 495 / Gene: ALPHA-LYTIC PROTEASE PREPROENZ / Plasmid: PALP12 (PBR322-DERIVATIVE) / Gene (production host): ALPHA-LYTIC PROTEASE PREPROENZYME / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Protein/peptide METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 442.271 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: METHOXYSUCCINYL-ALA-ALA-PRO-ALANINE BORONIC ACID
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGS IN WHICH THE C-TERMINAL CARBOXYL GROUP HAS ...INHIBITORY PEPTIDE BORONIC ACIDS ARE PEPTIDE ANALOGS IN WHICH THE C-TERMINAL CARBOXYL GROUP HAS BEEN REPLACED WITH THE BORONIC ACID GROUP (B(OH)2).
Has protein modificationY
Sequence detailsCHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPSIN FOR RESIDUES 15A - 245. CHAIN P ...CHAIN A RESIDUE NUMBERING IS DONE BY HOMOLOGY WITH CHYMOTRYPSIN FOR RESIDUES 15A - 245. CHAIN P INHIBITOR NUMBERING IS DONE BY ANALOGY TO PROTEASE SUBSTRATE NOMENCLATURE IN WHICH THE RESIDUE PRIOR TO THE SCISSILE BOND IS THE P1 RESIDUE, THE NEXT TOWARD THE N-TERMINUS IS THE P2 RESIDUE, ETC.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal
*PLUS
Density % sol: 48.3 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.4 M1reservoirLi2SO4
220 mMTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU AFC-6R / Detector: DIFFRACTOMETER / Date: Aug 5, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→17.5 Å / Num. obs: 11778 / % possible obs: 82 %

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Processing

Software
NameVersionClassification
RIGAKUAFC5 CONTROL SOFTWAREdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
RIGAKUAFC5 CONTROL SOFTWAREdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.13→17.5 Å / σ(F): 2
Details: THE METHOXYSUCCINYL PORTION OF THE INHIBITOR WAS DISORDERED AND NO COORDINATES ARE INCLUDED FOR IT IN THIS ENTRY
RfactorNum. reflection
Rwork0.134 -
obs0.134 11560
Refinement stepCycle: LAST / Resolution: 2.13→17.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 10 139 1560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
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
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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