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- PDB-3m7u: Crystal Structure of Alpha-Lytic Protease SB1+2 R64A/E182Q Mutant -

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Basic information

Entry
Database: PDB / ID: 3m7u
TitleCrystal Structure of Alpha-Lytic Protease SB1+2 R64A/E182Q Mutant
Components
  • Alpha-lytic protease
  • SELF-PROTEOLYSIS PRODUCT (RESIDUES 184-187)
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: 1.05 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

Downloads & links

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Assembly

Deposited unit
A: Alpha-lytic protease
B: SELF-PROTEOLYSIS PRODUCT (RESIDUES 184-187)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6426
Polymers20,2582
Non-polymers3844
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-53 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.396, 65.396, 79.856
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-211-

HOH

21A-643-

HOH

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Components

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


Mass: 19788.031 Da / Num. of mol.: 1 / Fragment: MATURE PROTEASE DOMAIN (RESIDUES 1-198) / Mutation: R64A, E182Q
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: Protein/peptide SELF-PROTEOLYSIS PRODUCT (RESIDUES 184-187)


Mass: 469.574 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
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: 1.03→46.196 Å / Num. all: 92399 / Num. obs: 91149 / % possible obs: 98.65 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 33.1 % / Biso Wilson estimate: 8.97 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 118.4
Reflection shellResolution: 1.03→1.05 Å / Redundancy: 18.1 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 9.5 / Rsym value: 0.644 / % 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: 1.05→46.196 Å / Isotropic thermal model: anisotropic / σ(F): 1.33 / Phase error: 16.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1638 2022 2.22 %
Rwork0.1406 --
obs0.1408 91149 98.65 %
all-91149 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.327 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso mean: 13.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.4705 Å20.4705 Å2-0.9933 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.05→46.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1418 0 20 527 1965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061562
X-RAY DIFFRACTIONf_angle_d1.1092133
X-RAY DIFFRACTIONf_dihedral_angle_d13.513541
X-RAY DIFFRACTIONf_chiral_restr0.066241
X-RAY DIFFRACTIONf_plane_restr0.004288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.07660.44791350.39195876X-RAY DIFFRACTION90
1.0766-1.10560.3211380.32246064X-RAY DIFFRACTION93
1.1056-1.13820.24951420.25426235X-RAY DIFFRACTION95
1.1382-1.17490.2291380.21936328X-RAY DIFFRACTION97
1.1749-1.21690.20881420.19646330X-RAY DIFFRACTION97
1.2169-1.26560.21561400.17836332X-RAY DIFFRACTION97
1.2656-1.32310.19131450.16966383X-RAY DIFFRACTION97
1.3231-1.39280.18731470.15656384X-RAY DIFFRACTION97
1.3928-1.480.16211420.15026410X-RAY DIFFRACTION98
1.48-1.59420.14961430.1436467X-RAY DIFFRACTION98
1.5942-1.75430.15441480.13576430X-RAY DIFFRACTION98
1.7543-2.00760.1581450.12156496X-RAY DIFFRACTION98
2.0076-2.52730.12881480.10616536X-RAY DIFFRACTION98
2.5273-14.60120.13221530.09836750X-RAY DIFFRACTION98

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