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- PDB-7co3: HtrA-type protease AlgWS227A with tripeptide -

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Basic information

Entry
Database: PDB / ID: 7co3
TitleHtrA-type protease AlgWS227A with tripeptide
Components
  • AlgW protein
  • TRP-VAL-PHE
KeywordsPEPTIDE BINDING PROTEIN / complex
Function / homology
Function and homology information


peptidase activity / periplasmic space / serine-type endopeptidase activity / proteolysis
Similarity search - Function
PDZ domain / Peptidase S1C / Trypsin-like peptidase domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Probable periplasmic serine endoprotease DegP-like
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, T. / Song, Y.J. / Bao, R.
CitationJournal: Mbio / Year: 2021
Title: Molecular Basis of the Versatile Regulatory Mechanism of HtrA-Type Protease AlgW from Pseudomonas aeruginosa.
Authors: Li, T. / Song, Y. / Luo, L. / Zhao, N. / He, L. / Kang, M. / Li, C. / Zhu, Y. / Shen, Y. / Zhao, C. / Yang, J. / Huang, Q. / Mou, X. / Zong, Z. / Yang, J. / Tang, H. / He, Y. / Bao, R.
History
DepositionAug 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: TRP-VAL-PHE
A: AlgW protein


Theoretical massNumber of molelcules
Total (without water)41,4732
Polymers41,4732
Non-polymers00
Water2,972165
1
C: TRP-VAL-PHE
A: AlgW protein

C: TRP-VAL-PHE
A: AlgW protein

C: TRP-VAL-PHE
A: AlgW protein


Theoretical massNumber of molelcules
Total (without water)124,4206
Polymers124,4206
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7630 Å2
ΔGint-47 kcal/mol
Surface area38510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.614, 96.614, 119.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21A-483-

HOH

31A-534-

HOH

41A-538-

HOH

51A-547-

HOH

61A-555-

HOH

71A-561-

HOH

81A-564-

HOH

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Components

#1: Protein/peptide TRP-VAL-PHE


Mass: 450.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein AlgW protein


Mass: 41022.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: algW, PA4446 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HVX1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.94 Å3/Da / Density % sol: 36.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.8M Sodium/Potassium Phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.898→39.49 Å / Num. obs: 49248 / % possible obs: 99.82 % / Redundancy: 28.5 % / Biso Wilson estimate: 25.71 Å2 / CC1/2: 0.958 / Net I/σ(I): 24.67
Reflection shellResolution: 1.898→1.996 Å / Num. unique obs: 2558 / CC1/2: 0.915

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOZ

1soz


Resolution: 1.9→39.49 Å / SU ML: 0.3098 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.815 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2695 3706 7.53 %
Rwork0.2335 45542 -
obs0.2362 49248 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.84 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 25 165 2371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01332231
X-RAY DIFFRACTIONf_angle_d1.50263026
X-RAY DIFFRACTIONf_chiral_restr0.0881363
X-RAY DIFFRACTIONf_plane_restr0.0083398
X-RAY DIFFRACTIONf_dihedral_angle_d13.84851337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.39551400.37331676X-RAY DIFFRACTION95.43
1.92-1.950.33831390.33831717X-RAY DIFFRACTION99.95
1.95-1.980.31581490.33771782X-RAY DIFFRACTION100
1.98-2.010.37931370.33311723X-RAY DIFFRACTION100
2.01-2.040.34311440.32621751X-RAY DIFFRACTION100
2.04-2.070.38951460.33171759X-RAY DIFFRACTION100
2.07-2.110.3511440.30741770X-RAY DIFFRACTION100
2.11-2.150.32251420.29281770X-RAY DIFFRACTION100
2.15-2.190.30411410.27431758X-RAY DIFFRACTION100
2.19-2.230.27811460.26911722X-RAY DIFFRACTION100
2.23-2.280.281440.25431747X-RAY DIFFRACTION100
2.28-2.330.29651470.24551764X-RAY DIFFRACTION100
2.33-2.390.28921430.25161779X-RAY DIFFRACTION100
2.39-2.460.30291450.24991729X-RAY DIFFRACTION100
2.46-2.530.2771400.22891765X-RAY DIFFRACTION100
2.53-2.610.2611460.24541768X-RAY DIFFRACTION100
2.61-2.70.28841420.22581739X-RAY DIFFRACTION100
2.7-2.810.28381440.22021736X-RAY DIFFRACTION100
2.81-2.940.28941370.231786X-RAY DIFFRACTION100
2.94-3.090.30611430.23161732X-RAY DIFFRACTION100
3.09-3.290.25971420.231768X-RAY DIFFRACTION100
3.29-3.540.21611460.20641753X-RAY DIFFRACTION100
3.54-3.90.22611400.19581747X-RAY DIFFRACTION100
3.9-4.460.22771490.1751752X-RAY DIFFRACTION100
4.46-5.620.22641330.19761771X-RAY DIFFRACTION100
5.62-39.490.24721370.21521778X-RAY DIFFRACTION99.95

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