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- PDB-7zjb: Structural and functional characterization of the bacterial lytic... -

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Basic information

Entry
Database: PDB / ID: 7zjb
TitleStructural and functional characterization of the bacterial lytic polysaccharide Monooxygenase ScLPMO10D
ComponentsPutative secreted cellulose-binding protein
KeywordsOXIDOREDUCTASE / LPMO / AA10
Function / homology: / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / metal ion binding / membrane / COPPER (II) ION / Secreted cellulose-binding protein
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsVotvik, A.K. / Rohr, A.K. / Stepnov, A.A. / Bissaro, B. / Sorlie, M. / Eijsink, V.G.H. / Forsberg, Z.
Funding support Denmark, Norway, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0055736 Denmark
Research Council of Norway301022 Norway
Research Council of Norway262853 Norway
CitationJournal: Sci Rep / Year: 2023
Title: Structural and functional characterization of the catalytic domain of a cell-wall anchored bacterial lytic polysaccharide monooxygenase from Streptomyces coelicolor.
Authors: Votvik, A.K. / Rohr, A.K. / Bissaro, B. / Stepnov, A.A. / Sorlie, M. / Eijsink, V.G.H. / Forsberg, Z.
History
DepositionApr 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 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
B: Putative secreted cellulose-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,21413
Polymers19,1671
Non-polymers1,04712
Water3,855214
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)59.080, 59.080, 145.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-205-

SO4

21B-205-

SO4

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Components

#1: Protein Putative secreted cellulose-binding protein


Mass: 19167.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO1734 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9S296
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.32 Å3/Da / Density % sol: 62.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 0.1 M sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97702 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97702 Å / Relative weight: 1
ReflectionResolution: 1.37→48.57 Å / Num. obs: 55188 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5
Reflection shellResolution: 1.37→1.42 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.369 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5301 / CC1/2: 0.789 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IF7

6if7


Resolution: 1.37→54.81 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.426 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15232 2712 4.9 %RANDOM
Rwork0.12934 ---
obs0.13045 52497 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 1.37→54.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 52 214 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131465
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171248
X-RAY DIFFRACTIONr_angle_refined_deg2.1041.6442012
X-RAY DIFFRACTIONr_angle_other_deg1.6841.5792913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg19.0675.693202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.87821.2962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75915195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.19158
X-RAY DIFFRACTIONr_chiral_restr0.110.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02315
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1222.048738
X-RAY DIFFRACTIONr_mcbond_other2.0922.041736
X-RAY DIFFRACTIONr_mcangle_it2.533.086925
X-RAY DIFFRACTIONr_mcangle_other2.4993.082925
X-RAY DIFFRACTIONr_scbond_it5.1652.55724
X-RAY DIFFRACTIONr_scbond_other4.012.407688
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2773.4461023
X-RAY DIFFRACTIONr_long_range_B_refined9.61926.8431635
X-RAY DIFFRACTIONr_long_range_B_other4.31925.5351574
X-RAY DIFFRACTIONr_rigid_bond_restr5.25332710
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.37→1.403 Å
RfactorNum. reflection% reflection
Rfree0.282 193 -
Rwork0.257 3636 -
obs--94.94 %

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