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- PDB-7co2: HtrA-type protease AlgW with tripeptide -

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Basic information

Entry
Database: PDB / ID: 7co2
TitleHtrA-type protease AlgW with tripeptide
Components
  • AlgW protein
  • TRP-VAL-PHE
KeywordsPEPTIDE BINDING PROTEIN / complex
Function / homology
Function and homology information


peptidase activity / 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
IMIDAZOLE / AlgW protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6264
Polymers41,4872
Non-polymers1382
Water2,900161
1
C: TRP-VAL-PHE
A: AlgW protein
hetero molecules

C: TRP-VAL-PHE
A: AlgW protein
hetero molecules

C: TRP-VAL-PHE
A: AlgW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,87712
Polymers124,4626
Non-polymers4156
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 area7870 Å2
ΔGint-42 kcal/mol
Surface area39320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.845, 95.845, 118.765
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-557-

HOH

21A-600-

HOH

31A-612-

HOH

41A-616-

HOH

51A-619-

HOH

61A-636-

HOH

71A-638-

HOH

81A-644-

HOH

91A-651-

HOH

101A-652-

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: 41036.914 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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.9 Å3/Da / Density % sol: 35.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NACl,0.1 M Tris 8.5, 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97891 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.098→39.18 Å / Num. obs: 35722 / % possible obs: 99.92 % / Redundancy: 26.5 % / Biso Wilson estimate: 34.75 Å2 / CC1/2: 1 / Net I/σ(I): 24.67
Reflection shellResolution: 2.098→2.173 Å / Num. unique obs: 1891 / CC1/2: 0.243 / % possible all: 99.58

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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: 2.1→39.18 Å / SU ML: 0.3245 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 26.4676 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2662 3561 9.97 %
Rwork0.2319 32161 -
obs0.2353 35722 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.48 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 35 161 2378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01112243
X-RAY DIFFRACTIONf_angle_d1.22793038
X-RAY DIFFRACTIONf_chiral_restr0.068362
X-RAY DIFFRACTIONf_plane_restr0.0076400
X-RAY DIFFRACTIONf_dihedral_angle_d20.90171340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.36051410.3571282X-RAY DIFFRACTION99.09
2.13-2.160.40541380.36271275X-RAY DIFFRACTION100
2.16-2.190.39421380.34861314X-RAY DIFFRACTION100
2.19-2.220.35931430.34651265X-RAY DIFFRACTION100
2.22-2.260.32821420.34251281X-RAY DIFFRACTION100
2.26-2.30.32231470.32681293X-RAY DIFFRACTION100
2.3-2.340.37381430.31211284X-RAY DIFFRACTION100
2.34-2.390.29581420.3151290X-RAY DIFFRACTION100
2.39-2.430.35691430.29171288X-RAY DIFFRACTION100
2.43-2.490.27861400.27961281X-RAY DIFFRACTION100
2.49-2.550.30651450.2691286X-RAY DIFFRACTION100
2.55-2.610.30441400.27671295X-RAY DIFFRACTION100
2.61-2.680.31061440.25251292X-RAY DIFFRACTION100
2.68-2.760.27771400.26581287X-RAY DIFFRACTION99.93
2.76-2.850.35531400.23231278X-RAY DIFFRACTION100
2.85-2.950.24351480.22751285X-RAY DIFFRACTION100
2.95-3.070.28681380.21611289X-RAY DIFFRACTION100
3.07-3.210.26811430.21521288X-RAY DIFFRACTION100
3.21-3.380.24041440.20641287X-RAY DIFFRACTION100
3.38-3.590.24081430.20061292X-RAY DIFFRACTION100
3.59-3.860.21791480.18881274X-RAY DIFFRACTION100
3.86-4.250.25011410.18331301X-RAY DIFFRACTION100
4.25-4.870.19771450.17881276X-RAY DIFFRACTION100
4.87-6.130.2241420.21531287X-RAY DIFFRACTION100
6.13-39.180.25121430.20941291X-RAY DIFFRACTION99.03

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