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- PDB-7sqx: Crystal Structure of Pseudomonas aeruginosa lytic polysaccharide ... -

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Basic information

Entry
Database: PDB / ID: 7sqx
TitleCrystal Structure of Pseudomonas aeruginosa lytic polysaccharide monooxygenase CbpD
ComponentsChitin-binding protein CbpD
KeywordsOXIDOREDUCTASE / LPMO virulence factor / Type II secretion
Function / homology
Function and homology information


protein transport by the Sec complex / protein secretion by the type II secretion system / chitin binding / extracellular space
Similarity search - Function
N-acetylglucosamine binding protein A domain 2 / N-acetylglucosamine binding protein domain 2 / : / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set
Similarity search - Domain/homology
AMMONIUM ION / Chitin-binding protein CbpD
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDade, C. / Douzi, B. / Ball, G. / Voulhoux, R. / Forest, K.T.
Funding support France, 2items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA)WIS03052 France
Agence Nationale de la Recherche (ANR)ANR-14-CE09-0027-01 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: The crystal structure of CbpD clarifies substrate-specificity motifs in chitin-active lytic polysaccharide monooxygenases.
Authors: Dade, C.M. / Douzi, B. / Cambillau, C. / Ball, G. / Voulhoux, R. / Forest, K.T.
History
DepositionNov 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references
Category: citation / citation_author / pdbx_related_exp_data_set
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitin-binding protein CbpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7134
Polymers40,6591
Non-polymers543
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Chitin-binding protein CbpD
hetero molecules

A: Chitin-binding protein CbpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4268
Polymers81,3182
Non-polymers1086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+y+1,y,-z+1/31
Buried area2190 Å2
ΔGint-4 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.770, 85.770, 90.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: -y,-x,-z+2/3
#5: -x+y,y,-z+1/3
#6: x,x-y,-z

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Components

#1: Protein Chitin-binding protein CbpD / Protease LasD


Mass: 40658.996 Da / Num. of mol.: 1
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: cbpD, lasD, PA0852 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I589
#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 mM di-ammonium tartrate, 20% (w/v) PEG 3350, 20mM Tris, 100mM NaCl, pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0087 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0087 Å / Relative weight: 1
ReflectionResolution: 2.9→42.885 Å / Num. obs: 8655 / % possible obs: 99.98 % / Redundancy: 11.2 % / Biso Wilson estimate: 71.9 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.154 / Net I/σ(I): 11.87
Reflection shellResolution: 2.9→2.97 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 642 / CC1/2: 0.568 / R split: 1.543 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEJuly 4, 2012data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ab initio model

Resolution: 3→38.78 Å / SU ML: 0.447 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.9658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 781 9.98 %
Rwork0.2097 7041 -
obs0.2135 7822 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.68 Å2
Refinement stepCycle: LAST / Resolution: 3→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2215 0 3 5 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00262274
X-RAY DIFFRACTIONf_angle_d0.57213106
X-RAY DIFFRACTIONf_chiral_restr0.0432330
X-RAY DIFFRACTIONf_plane_restr0.0042419
X-RAY DIFFRACTIONf_dihedral_angle_d15.7032797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.39591300.3511157X-RAY DIFFRACTION100
3.19-3.430.34451260.28131167X-RAY DIFFRACTION99.92
3.43-3.780.27841280.24711165X-RAY DIFFRACTION100
3.78-4.320.22811310.19831169X-RAY DIFFRACTION100
4.33-5.450.21331350.17851173X-RAY DIFFRACTION100
5.45-38.780.21731310.17421210X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 27.1560337411 Å / Origin y: 5.89597124962 Å / Origin z: -11.8632720435 Å
111213212223313233
T0.625829208046 Å2-0.147858408335 Å20.0796427400456 Å2-0.564557334544 Å2-0.142865951108 Å2--0.677014233255 Å2
L0.993179127843 °20.235429030204 °21.1043817759 °2-1.57400842648 °2-1.28307331698 °2--4.20856083261 °2
S-0.0229436525338 Å °0.168390399471 Å °-0.168587995467 Å °-0.506461875614 Å °0.157539656515 Å °0.0553131399913 Å °0.823177757343 Å °-0.146068519439 Å °-0.139882278413 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 296)

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