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- PDB-1boq: PRO REGION C-TERMINUS: PROTEASE ACTIVE SITE INTERACTIONS ARE CRIT... -

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Basic information

Entry
Database: PDB / ID: 1boq
TitlePRO REGION C-TERMINUS: PROTEASE ACTIVE SITE INTERACTIONS ARE CRITICAL IN CATALYZING THE FOLDING OF ALPHA-LYTIC PROTEASE
ComponentsPROTEIN (ALPHA-LYTIC PROTEASE)
KeywordsHYDROLASE / SERINE PROTEASE / FOLDING MUTANT
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPeters, R.J. / Shiau, A.K. / Sohl, J.L. / Anderson, D.E. / Tang, G. / Silen, J.L. / Agard, D.A.
Citation
Journal: Biochemistry / Year: 1998
Title: Pro region C-terminus:protease active site interactions are critical in catalyzing the folding of alpha-lytic protease.
Authors: Peters, R.J. / Shiau, A.K. / Sohl, J.L. / Anderson, D.E. / Tang, G. / Silen, J.L. / Agard, D.A.
#1: Journal: Biochemistry / Year: 1991
Title: Structural Basis for Broad Specificity in Alpha-Lytic Protease
Authors: Bone, R. / Fujishige, 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, C.A. / 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 A Resolution. Analysis of Hydrogen Bonding and Solvent Structure
Authors: Fujinaga, M. / Delbaere, L.T. / Brayer, G.D. / James, M.N.
#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. / James, M.N.
History
DepositionAug 5, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 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: PROTEIN (ALPHA-LYTIC PROTEASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0813
Polymers19,8891
Non-polymers1922
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.200, 66.200, 80.200
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 PROTEIN (ALPHA-LYTIC PROTEASE)


Mass: 19889.156 Da / Num. of mol.: 1 / Mutation: V119I / Source method: isolated from a natural source / Source: (natural) Lysobacter enzymogenes (bacteria) / Strain: 495 / 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.: 136 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE NUMBERING IS BY HOMOLOGY WITH CHYMOTRYPSIN FOR CHAIN A RESIDUES 15A - 245.

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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: 2.55 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop / Details: ambient temperature
Components of the solutions
*PLUS
Conc.: 1.3 M / Common name: lithium sulfate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 25, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 33422 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 2.2→2.2 Å / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ALP

2alp


Resolution: 2.1→6 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 4218 10 %RANDOM
Rwork0.159 ---
obs0.159 42177 90.4 %-
Displacement parametersBiso mean: 15.2 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 10 408 2162
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_deg2.89
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

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