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- PDB-7xfs: MucP PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 7xfs
TitleMucP PDZ1 domain
ComponentsPutative zinc metalloprotease PA3649
KeywordsLYASE / MucP / alginate biosynthesis / Pseudomonas aeruginosa PAO1 / Crystal structure.
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding / plasma membrane
Similarity search - Function
Peptidase M50, putative membrane-associated zinc metallopeptidase / Peptidase M50 / Peptidase family M50 / PDZ domain / PDZ domain 6 / PDZ domain / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Putative zinc metalloprotease PA3649
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsLou, X. / Li, S. / Zhang, Q. / Bartlam, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800627 China
National Natural Science Foundation of China (NSFC)31870053 China
CitationJournal: To Be Published
Title: MucP PDZ1 domain
Authors: Lou, X. / Li, S. / Zhang, Q. / Bartlam, M.
History
DepositionApr 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative zinc metalloprotease PA3649
B: Putative zinc metalloprotease PA3649


Theoretical massNumber of molelcules
Total (without water)20,4572
Polymers20,4572
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.640, 49.466, 100.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Putative zinc metalloprotease PA3649 / MucP


Mass: 10228.382 Da / Num. of mol.: 2 / Fragment: PDZ1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3649 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9HXY3, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG 300, 0.1M sodium arsenate pH 6.5, 0.2M calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. obs: 78318 / % possible obs: 98.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.07 Å2 / Rpim(I) all: 0.024 / Net I/σ(I): 30.5
Reflection shellResolution: 1.06→1.08 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3570 / Rpim(I) all: 0.175 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ID1

3id1


Resolution: 1.06→49.47 Å / SU ML: 0.1224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.1769
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1734 1999 2.66 %
Rwork0.1504 73012 -
obs0.151 75011 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.98 Å2
Refinement stepCycle: LAST / Resolution: 1.06→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1442 0 0 238 1680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00761468
X-RAY DIFFRACTIONf_angle_d0.94212002
X-RAY DIFFRACTIONf_chiral_restr0.0744224
X-RAY DIFFRACTIONf_plane_restr0.0098272
X-RAY DIFFRACTIONf_dihedral_angle_d5.1558206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.090.3746960.34793477X-RAY DIFFRACTION64.1
1.09-1.120.24161170.27194284X-RAY DIFFRACTION78.87
1.12-1.150.23161320.20544809X-RAY DIFFRACTION88.79
1.15-1.190.15681450.15535294X-RAY DIFFRACTION97.19
1.19-1.230.15781470.13635376X-RAY DIFFRACTION98.91
1.23-1.280.16221480.13615412X-RAY DIFFRACTION99.04
1.28-1.330.18151480.14185441X-RAY DIFFRACTION99.55
1.33-1.40.19431490.15035429X-RAY DIFFRACTION99.36
1.4-1.490.17081500.14415487X-RAY DIFFRACTION99.73
1.49-1.610.1471510.13125481X-RAY DIFFRACTION99.91
1.61-1.770.15621510.13855536X-RAY DIFFRACTION100
1.77-2.030.16031520.14115538X-RAY DIFFRACTION100
2.03-2.550.14951530.14525603X-RAY DIFFRACTION99.98
2.55-49.470.19041600.15675845X-RAY DIFFRACTION99.82

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