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- PDB-7co5: HtrA-type protease AlgW with decapeptide -

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Basic information

Entry
Database: PDB / ID: 7co5
TitleHtrA-type protease AlgW with decapeptide
Components
  • AlgW protein
  • decapeptide SVRDELRWVF
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
IMIDAZOLE / Probable periplasmic serine endoprotease DegP-like
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.345 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: decapeptide SVRDELRWVF
H: AlgW protein
A: decapeptide SVRDELRWVF
B: AlgW protein
C: decapeptide SVRDELRWVF
D: AlgW protein
E: decapeptide SVRDELRWVF
F: AlgW protein
I: decapeptide SVRDELRWVF
J: AlgW protein
K: decapeptide SVRDELRWVF
L: AlgW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,25018
Polymers246,83512
Non-polymers4156
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26160 Å2
ΔGint-125 kcal/mol
Surface area85340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.120, 130.837, 250.364
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and resid 5 through 10)
21(chain C and resid 5 through 10)
31chain E
41chain G
51chain I
12chain B
22chain D
32chain F
42chain H
52chain J
62chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPHEPHE(chain A and resid 5 through 10)AC5 - 105 - 10
21GLUGLUPHEPHE(chain C and resid 5 through 10)CE5 - 105 - 10
31GLUGLUPHEPHEchain EEG5 - 105 - 10
41GLUGLUPHEPHEchain GGA5 - 105 - 10
51GLUGLUPHEPHEchain III5 - 105 - 10
12VALVALPROPROchain BBD53 - 37753 - 377
22VALVALPROPROchain DDF53 - 37753 - 377
32VALVALPROPROchain FFH53 - 37753 - 377
42VALVALPROPROchain HHB53 - 37753 - 377
52VALVALPROPROchain JJJ53 - 37753 - 377
62VALVALPROPROchain LLL53 - 37753 - 377

NCS ensembles :
ID
1
2

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Components

#1: Protein/peptide
decapeptide SVRDELRWVF


Mass: 1308.485 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
AlgW protein / Probable periplasmic serine endoprotease DegP-like / Protease Do


Mass: 39830.680 Da / Num. of mol.: 6
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) / Strain (production host): BL21(DE3) / References: UniProt: Q9HVX1
#3: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate PH 7.0, 5% 2-Propanol, 0.1M Imidazole PH 7.0, 8% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.345→34.5 Å / Num. obs: 213255 / % possible obs: 96.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 14.08 Å2 / CC1/2: 0.796 / Net I/σ(I): 2.96
Reflection shellResolution: 2.345→2.429 Å / Num. unique obs: 11425 / CC1/2: 0.262

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOZ

1soz


Resolution: 2.345→34.5 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2892 3403 1.6 %
Rwork0.2681 209852 -
obs0.2684 213255 84.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.32 Å2 / Biso mean: 33.657 Å2 / Biso min: 0.48 Å2
Refinement stepCycle: final / Resolution: 2.345→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14730 0 30 316 15076
Biso mean--33.14 23.43 -
Num. residues----1991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A132X-RAY DIFFRACTION28.575TORSIONAL
12C132X-RAY DIFFRACTION28.575TORSIONAL
13E132X-RAY DIFFRACTION28.575TORSIONAL
14G132X-RAY DIFFRACTION28.575TORSIONAL
15I132X-RAY DIFFRACTION28.575TORSIONAL
21B8921X-RAY DIFFRACTION28.575TORSIONAL
22D8921X-RAY DIFFRACTION28.575TORSIONAL
23F8921X-RAY DIFFRACTION28.575TORSIONAL
24H8921X-RAY DIFFRACTION28.575TORSIONAL
25J8921X-RAY DIFFRACTION28.575TORSIONAL
26L8921X-RAY DIFFRACTION28.575TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3454-2.37890.35611090.3456692766
2.3789-2.41440.36631310.3588798378
2.4144-2.45210.35851310.349822379
2.4521-2.49230.37971330.376814679
2.4923-2.53530.44571270.3748806178
2.5353-2.58130.35141390.3351812078
2.5813-2.6310.35371360.3478817879
2.631-2.68470.4041220.3663810178
2.6847-2.7430.39111290.3565780075
2.743-2.80680.38211190.3519815279
2.8068-2.87690.40991370.3354823779
2.8769-2.95470.35771370.3304854083
2.9547-3.04160.36141450.3142880485
3.0416-3.13970.35321450.2977883486
3.1397-3.25180.34261500.2803909688
3.2518-3.38190.28071470.2554926589
3.3819-3.53570.28581470.2377926389
3.5357-3.72190.22931520.224947592
3.7219-3.95480.22761540.209925789
3.9548-4.25960.211590.1844961293
4.2596-4.68730.18481660.164992496
4.6873-5.36340.21351640.1802996496
5.3634-6.74910.24031620.2193980195

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