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- PDB-7co7: HtrA-type protease AlgWS227A with decapeptide -

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Basic information

Entry
Database: PDB / ID: 7co7
TitleHtrA-type protease AlgWS227A 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
Probable periplasmic serine endoprotease DegP-like
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 4, 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: decapeptide SVRDELRWVF
D: AlgW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9063
Polymers35,6852
Non-polymers2211
Water1,47782
1
C: decapeptide SVRDELRWVF
D: AlgW protein
hetero molecules

C: decapeptide SVRDELRWVF
D: AlgW protein
hetero molecules

C: decapeptide SVRDELRWVF
D: AlgW protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,7189
Polymers107,0546
Non-polymers6643
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
Buried area9980 Å2
ΔGint-22 kcal/mol
Surface area45310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.100, 179.100, 179.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number196
Space group name H-MF23
Space group name HallF223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x,y+1/2,z+1/2
#14: z,x+1/2,y+1/2
#15: y,z+1/2,x+1/2
#16: -y,-z+1/2,x+1/2
#17: z,-x+1/2,-y+1/2
#18: -y,z+1/2,-x+1/2
#19: -z,-x+1/2,y+1/2
#20: -z,x+1/2,-y+1/2
#21: y,-z+1/2,-x+1/2
#22: x,-y+1/2,-z+1/2
#23: -x,y+1/2,-z+1/2
#24: -x,-y+1/2,z+1/2
#25: x+1/2,y,z+1/2
#26: z+1/2,x,y+1/2
#27: y+1/2,z,x+1/2
#28: -y+1/2,-z,x+1/2
#29: z+1/2,-x,-y+1/2
#30: -y+1/2,z,-x+1/2
#31: -z+1/2,-x,y+1/2
#32: -z+1/2,x,-y+1/2
#33: y+1/2,-z,-x+1/2
#34: x+1/2,-y,-z+1/2
#35: -x+1/2,y,-z+1/2
#36: -x+1/2,-y,z+1/2
#37: x+1/2,y+1/2,z
#38: z+1/2,x+1/2,y
#39: y+1/2,z+1/2,x
#40: -y+1/2,-z+1/2,x
#41: z+1/2,-x+1/2,-y
#42: -y+1/2,z+1/2,-x
#43: -z+1/2,-x+1/2,y
#44: -z+1/2,x+1/2,-y
#45: y+1/2,-z+1/2,-x
#46: x+1/2,-y+1/2,-z
#47: -x+1/2,y+1/2,-z
#48: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11D-517-

HOH

21D-518-

HOH

31D-537-

HOH

41D-553-

HOH

51D-560-

HOH

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Components

#1: Protein/peptide decapeptide SVRDELRWVF


Mass: 1308.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein AlgW protein


Mass: 34376.168 Da / Num. of mol.: 1 / Mutation: S227A
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-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID / CAPS (buffer)


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 3.39 Å3/Da / Density % sol: 63.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 30% PEG 400, 100mM CAPS/Sodium hydrochloric PH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.6→34.47 Å / Num. obs: 28555 / % possible obs: 99.96 % / Redundancy: 30.3 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 1 / Net I/σ(I): 22.53
Reflection shellResolution: 2.6→2.694 Å / Num. unique obs: 1500 / CC1/2: 0.146

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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: 2.6→34.47 Å / SU ML: 0.3485 / Cross valid method: FREE R-VALUE / σ(F): 1.69 / Phase error: 23.649 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2383 2812 9.85 %
Rwork0.1974 25743 -
obs0.2014 28555 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2479 0 14 82 2575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922532
X-RAY DIFFRACTIONf_angle_d1.16613435
X-RAY DIFFRACTIONf_chiral_restr0.0599401
X-RAY DIFFRACTIONf_plane_restr0.0074453
X-RAY DIFFRACTIONf_dihedral_angle_d22.76791530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.650.31971430.33081305X-RAY DIFFRACTION100
2.65-2.690.34391480.34281338X-RAY DIFFRACTION100
2.69-2.750.33171440.32831255X-RAY DIFFRACTION100
2.75-2.80.33731380.31221274X-RAY DIFFRACTION100
2.8-2.860.28751460.28521270X-RAY DIFFRACTION100
2.86-2.930.30461390.27141265X-RAY DIFFRACTION100
2.93-30.33491300.25351309X-RAY DIFFRACTION100
3-3.080.28451360.24171289X-RAY DIFFRACTION100
3.08-3.170.27321380.24181282X-RAY DIFFRACTION100
3.17-3.280.29151410.23551304X-RAY DIFFRACTION100
3.28-3.390.28021380.21651260X-RAY DIFFRACTION100
3.39-3.530.27281480.19721306X-RAY DIFFRACTION100
3.53-3.690.24011400.1881259X-RAY DIFFRACTION100
3.69-3.880.26111320.19221284X-RAY DIFFRACTION100
3.88-4.130.25191380.17351311X-RAY DIFFRACTION100
4.13-4.450.19451370.1511269X-RAY DIFFRACTION100
4.45-4.890.18771460.1381294X-RAY DIFFRACTION100
4.89-5.60.18631430.15671289X-RAY DIFFRACTION100
5.6-7.040.21031420.18551296X-RAY DIFFRACTION100
7.04-34.470.19151450.1751284X-RAY DIFFRACTION99.31

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