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- PDB-2alp: REFINED STRUCTURE OF ALPHA-LYTIC PROTEASE AT 1.7 ANGSTROMS RESOLU... -

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Basic information

Entry
Database: PDB / ID: 2alp
TitleREFINED STRUCTURE OF ALPHA-LYTIC PROTEASE AT 1.7 ANGSTROMS RESOLUTION. ANALYSIS OF HYDROGEN BONDING AND SOLVENT STRUCTURE
ComponentsALPHA-LYTIC PROTEASE
KeywordsHYDROLASE (SERINE PROTEINASE)
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
Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsFujinaga, M. / Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Refined structure of alpha-lytic protease at 1.7 A resolution. Analysis of hydrogen bonding and solvent structure.
Authors: Fujinaga, M. / Delbaere, L.T. / Brayer, G.D. / James, M.N.
#1: 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.
#2: Journal: Nature / Year: 1979
Title: Comparison of the Predicted Model of Alph-Lytic Protease with the X-Ray Structure
Authors: Delbaere, L.T.J. / Brayer, G.D. / James, M.N.G.
#3: Journal: Can.J.Biochem. / Year: 1978
Title: Amino Acid Sequence Alignment of Bacterial and Mammalian Pancreatic Serine Proteases Based on Topological Equivalences
Authors: James, M.N.G. / Delbaere, L.T.J. / Brayer, G.D.
History
DepositionMar 7, 1985Processing site: BNL
SupersessionJul 17, 1985ID: 1ALP
Revision 1.0Jul 17, 1985Provider: 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 / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0673
Polymers19,8751
Non-polymers1922
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.210, 66.210, 80.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUE 95 IS A CIS-PROLINE.

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Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 19875.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal grow
*PLUS
pH: 6.1 / Method: microdialysis / Details: Brayer, G.D., (1979) J.Mol.Biol., 131, 743.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 M11Li2SO4
210 mg/mlprotein12

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Data collection

Reflection
*PLUS

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Processing

RefinementResolution: 1.7→8 Å / Rfactor Rwork: 0.131 / σ(I): 2
Refinement stepCycle: LAST / Resolution: 1.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 10 156 1557
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d0.03
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Num. reflection obs: 14996 / σ(I): 2 / Highest resolution: 1.7 Å / Lowest resolution: 8 Å / Rfactor obs: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_angle_d0.02
X-RAY DIFFRACTIONo_planar_d0.020.033
X-RAY DIFFRACTIONo_plane_restr0.0150.018
X-RAY DIFFRACTIONo_chiral_restr0.10.188

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