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- PDB-2ull: MULTIPLE CONFORMATION STRUCTURE OF ALPHA-LYTIC PROTEASE AT 120 K -

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Basic information

Entry
Database: PDB / ID: 2ull
TitleMULTIPLE CONFORMATION STRUCTURE OF ALPHA-LYTIC PROTEASE AT 120 K
ComponentsALPHA-LYTIC PROTEASE
KeywordsSERINE PROTEASE / HYDROLASE / ZYMOGEN / PROTEASE PRECURSOR
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 / REFINEMENT OF 2ALP / Resolution: 1.5 Å
AuthorsRader, S.D. / Agard, D.A.
Citation
Journal: Protein Sci. / Year: 1997
Title: Conformational substates in enzyme mechanism: the 120 K structure of alpha-lytic protease at 1.5 A resolution.
Authors: Rader, S.D. / Agard, D.A.
#1: Journal: Biochemistry / Year: 1991
Title: Structural Basis for Broad Specificity in Alpha-Lytic Protease Mutants
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
DepositionNov 26, 1996Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Version format compliance
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 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: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3275
Polymers19,8751
Non-polymers4514
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.800, 65.800, 79.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Number of models16

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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
Details: THE ELECTRON DENSITY WAS MODELED WITH 16 CONFORMATIONS OF THE ENTIRE PROTEIN
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 48.2 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
21.3 M1reservoirLi2SO4
320 mMTris-HCl1reservoir

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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: Aug 21, 1992 / Details: DUAL SLIT
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 33422 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 5.8 Å2 / Rsym value: 0.059
Reflection shellResolution: 1.5→1.57 Å / % possible all: 99.1
Reflection
*PLUS
Num. measured all: 148867 / Rmerge(I) obs: 0.059

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: REFINEMENT OF 2ALP
Starting model: PDB ENTRY 2ALP

2alp


Resolution: 1.5→6 Å / Isotropic thermal model: FIXED B'S / Cross valid method: THROUGHOUT / σ(F): 0
Details: ELECTRON DENSITY WAS MODELED WITH 16 CONFORMATIONS OF THE ENTIRE PROTEIN. OCCUPANCIES FOR ALL ATOMS WERE SET TO 1/16. EACH CONFORMATION IS REPRESENTED AS A SEPARATE MODEL. THE DEPOSITOR ...Details: ELECTRON DENSITY WAS MODELED WITH 16 CONFORMATIONS OF THE ENTIRE PROTEIN. OCCUPANCIES FOR ALL ATOMS WERE SET TO 1/16. EACH CONFORMATION IS REPRESENTED AS A SEPARATE MODEL. THE DEPOSITOR PROVIDED ONE SET OF HETATM RECORDS. IN ORDER TO FOLLOW PDB FORMAT REQUIREMENTS, THE SAME HETATM RECORDS WERE INCLUDED IN EACH MODEL. NOTE THAT THE OCCUPANCY OF THE HETATM RECORDS WAS NOT DIVIDED BY 16.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 3147 10 %RANDOM
Rwork0.165 ---
obs0.165 31458 99 %-
Displacement parametersBiso mean: 5.4 Å2
Refinement stepCycle: LAST / Resolution: 1.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1391 0 23 301 1715
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_deg1.7
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_d1.31
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
LS refinement shellResolution: 1.5→1.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.1963 426 10 %
Rwork0.1897 3476 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.155 / Rfactor Rfree: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31

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