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- PDB-7xfu: MucP PDZ2 domain with peptide GPAVLA -

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Basic information

Entry
Database: PDB / ID: 7xfu
TitleMucP PDZ2 domain with peptide GPAVLA
ComponentsPutative zinc metalloprotease PA3649,peptide GPAVLA
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 PDZ2 domain with peptide GPAVLA
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,peptide GPAVLA
B: Putative zinc metalloprotease PA3649,peptide GPAVLA


Theoretical massNumber of molelcules
Total (without water)19,5862
Polymers19,5862
Non-polymers00
Water4,450247
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)34.865, 34.865, 114.467
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: Protein Putative zinc metalloprotease PA3649,peptide GPAVLA / MucP


Mass: 9793.170 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PDZ2 domain with peptide GPAVLA
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria), (gene. exp.) synthetic construct (others)
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.: 247 / 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: 1.78 Å3/Da / Density % sol: 30.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate

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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: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 20550 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 13.42 Å2 / Rpim(I) all: 0.055 / Net I/σ(I): 14
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 982 / Rpim(I) all: 0.161 / % possible all: 98.6

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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: 7XFT

7xft


Resolution: 1.53→34.87 Å / SU ML: 0.1437 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 23.1309
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 2001 9.85 %
Rwork0.1876 18307 -
obs0.191 20308 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.99 Å2
Refinement stepCycle: LAST / Resolution: 1.53→34.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 0 255 1599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00651364
X-RAY DIFFRACTIONf_angle_d0.91851848
X-RAY DIFFRACTIONf_chiral_restr0.0613216
X-RAY DIFFRACTIONf_plane_restr0.0076248
X-RAY DIFFRACTIONf_dihedral_angle_d5.2221202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.28491250.22961135X-RAY DIFFRACTION89.11
1.57-1.610.23531410.20411296X-RAY DIFFRACTION97.03
1.61-1.660.26111440.19711329X-RAY DIFFRACTION99.39
1.66-1.710.2361450.2061295X-RAY DIFFRACTION99.93
1.71-1.770.27041360.19271334X-RAY DIFFRACTION99.73
1.77-1.840.21921450.20071338X-RAY DIFFRACTION100
1.84-1.930.25411410.18921311X-RAY DIFFRACTION100
1.93-2.030.25061440.19291317X-RAY DIFFRACTION100
2.03-2.160.21591450.18741331X-RAY DIFFRACTION100
2.16-2.320.22741440.1841328X-RAY DIFFRACTION100
2.32-2.560.21751490.19661294X-RAY DIFFRACTION100
2.56-2.930.24441520.19561341X-RAY DIFFRACTION99.87
2.93-3.690.19791440.1721317X-RAY DIFFRACTION99.8
3.69-34.870.17691460.17411341X-RAY DIFFRACTION99.73
Refinement TLS params.Method: refined / Origin x: -5.98260343042 Å / Origin y: 11.7661269481 Å / Origin z: -9.0064713531 Å
111213212223313233
T0.102478107497 Å2-0.0173195676047 Å20.00624710620276 Å2-0.0979541672383 Å2-0.00510279805126 Å2--0.107026611841 Å2
L0.0447551964294 °20.0350116365069 °20.0215113088224 °2-0.0442649864934 °20.0167114149925 °2--0.202294212242 °2
S-0.00122611841199 Å °-0.00887282163776 Å °-0.00608460174342 Å °-0.0097590694434 Å °-0.00187115764962 Å °0.00983098531982 Å °0.0070476649024 Å °-0.00997428159988 Å °-0.00787751109099 Å °
Refinement TLS groupSelection details: all

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