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- PDB-3m7t: Crystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant -

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Basic information

Entry
Database: PDB / ID: 3m7t
TitleCrystal Structure of Alpha-Lytic Protease SB2+3 E8A/R105S Mutant
ComponentsAlpha-lytic protease
KeywordsHYDROLASE / Disulfide bond / Protease / Serine protease / Zymogen
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: 1.55 Å
AuthorsAgard, D.A. / Erciyas Bailey, F.P. / Waddling, C.A.
Citation
Journal: To be Published
Title: Quantifying protein unfolding cooperativity with acid sensitive probes: Interdomain salt bridge contributions to unfolding cooperativity are combined efficiently in alpha-Lytic Protease
Authors: Erciyas Bailey, F.P. / Waddling, C.A. / Agard, D.A.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain.
Authors: Fuhrmann, C.N. / Kelch, B.A. / Ota, N. / Agard, D.A.
#2: 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.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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: Alpha-lytic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3197
Polymers19,7471
Non-polymers5726
Water8,071448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.015, 66.015, 79.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-609-

HOH

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Components

#1: Protein Alpha-lytic protease / Alpha-lytic endopeptidase


Mass: 19746.979 Da / Num. of mol.: 1 / Fragment: MATURE PROTEASE DOMAIN (RESIDUES 1-198) / Mutation: E8A, R105S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Gene: alpha-LP, Lysobacter / Plasmid: PALP12 / Production host: Escherichia coli (E. coli) / References: UniProt: P00778, alpha-lytic endopeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.3 M lithium sulfate, 20 mM Tris sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2009 / Details: Double Crystal Si(111)
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.55→57.171 Å / Num. all: 29718 / Num. obs: 29042 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 36.575
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.676 / Num. unique all: 1461 / Rsym value: 0.457 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: dev_328)model building
PHENIX(phenix.refine: dev_328)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXdev_328phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1SSX

1ssx


Resolution: 1.55→33.008 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: TWIN_LSQ_F
Details: protein atoms refined anisotropically, water atoms refined isotropically
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1482 5.13 %random
Rwork0.136 ---
obs0.1382 28909 97.4 %-
all-29718 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.419 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8581 Å20.8581 Å2-1.7161 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.008 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 31 448 1861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041489
X-RAY DIFFRACTIONf_angle_d0.9052030
X-RAY DIFFRACTIONf_dihedral_angle_d11.376497
X-RAY DIFFRACTIONf_chiral_restr0.064230
X-RAY DIFFRACTIONf_plane_restr0.003269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.55-1.60610.25151380.1742804280495
1.6061-1.67040.25461460.15662763276395
1.6704-1.74630.17971500.16092768276895
1.7463-1.83830.18641620.14412777277794
1.8383-1.95340.23951440.16172747274794
1.9534-2.1040.20151640.13762769276994
2.104-2.31540.23841070.13952399239981
2.3154-2.64970.20051640.13832823282394
2.6497-3.33530.18351660.12542826282694
3.3353-18.82670.1771320.1062734273487

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