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Basic information

Entry
Database: PDB / ID: 7xft
TitleMucP PDZ2 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
VALINE / Putative zinc metalloprotease PA3649
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5747
Polymers9,3421
Non-polymers2326
Water2,414134
1
A: Putative zinc metalloprotease PA3649
hetero molecules

A: Putative zinc metalloprotease PA3649
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,14714
Polymers18,6832
Non-polymers46412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area1840 Å2
ΔGint-105 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.312, 70.660, 50.376
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Putative zinc metalloprotease PA3649 / MucP


Mass: 9341.611 Da / Num. of mol.: 1 / Fragment: PDZ2 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: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 8000, 0.1M sodium arsenate, 0.2M thiamine

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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: 1.21→50 Å / Num. obs: 27025 / % possible obs: 99.3 % / Redundancy: 12.7 % / Biso Wilson estimate: 13.24 Å2 / Rpim(I) all: 0.022 / Net I/σ(I): 48.2
Reflection shellResolution: 1.21→1.23 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 6.2 / Num. unique obs: 1320 / Rpim(I) all: 0.091 / % possible all: 96.2

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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: 3ID2

3id2


Resolution: 1.21→24.66 Å / SU ML: 0.1134 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 17.2961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1881 1977 7.41 %
Rwork0.1666 24708 -
obs0.1682 26685 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.21→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 13 136 781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079646
X-RAY DIFFRACTIONf_angle_d0.9693872
X-RAY DIFFRACTIONf_chiral_restr0.08499
X-RAY DIFFRACTIONf_plane_restr0.0154118
X-RAY DIFFRACTIONf_dihedral_angle_d6.532294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.240.18421320.17421648X-RAY DIFFRACTION93.24
1.24-1.270.1991380.16631707X-RAY DIFFRACTION95.6
1.27-1.310.19491380.15971699X-RAY DIFFRACTION96.13
1.31-1.350.17611380.15271729X-RAY DIFFRACTION97.14
1.35-1.40.19751370.15181722X-RAY DIFFRACTION97.79
1.4-1.460.20881400.15041746X-RAY DIFFRACTION98.23
1.46-1.530.19431400.14541764X-RAY DIFFRACTION98.6
1.53-1.610.1671420.14261788X-RAY DIFFRACTION99.13
1.61-1.710.16691420.14781771X-RAY DIFFRACTION99.69
1.71-1.840.17921420.1561779X-RAY DIFFRACTION99.84
1.84-2.020.18191460.1561811X-RAY DIFFRACTION99.9
2.02-2.320.15571430.15771806X-RAY DIFFRACTION99.85
2.32-2.920.20561480.17251835X-RAY DIFFRACTION99.8
2.92-24.660.19941510.18621903X-RAY DIFFRACTION99.52

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