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- PDB-6uav: Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanas... -

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Basic information

Entry
Database: PDB / ID: 6uav
TitleCrystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Pseudomonas viridiflava (PvGH128_II)
ComponentsGlyco_hydro_cc domain-containing protein
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyfungal-type cell wall polysaccharide metabolic process / : / Uncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesPseudomonas viridiflava (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsSantos, C.R. / Costa, P.A.C.R. / Lima, E.A. / Mandelli, F. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family.
Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyco_hydro_cc domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9815
Polymers29,6001
Non-polymers3804
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.663, 33.648, 84.259
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

SO4

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 29600.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas viridiflava (bacteria) / Gene: CFBP1590__2373 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Y6JJH6
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: ammonium sulfate 2 M bis-tris 0.1 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.23986 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23986 Å / Relative weight: 1
ReflectionResolution: 1.5→43.45 Å / Num. obs: 36444 / % possible obs: 99.2 % / Redundancy: 5.38 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.1 / Net I/σ(I): 12.19
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 5.06 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 5775 / CC1/2: 0.702 / Rrim(I) all: 0.941 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→40.33 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.957 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20034 1823 5 %RANDOM
Rwork0.17077 ---
obs0.17224 34621 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.13 Å2
2--1.67 Å20 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.5→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 21 230 2342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132199
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171915
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.6373005
X-RAY DIFFRACTIONr_angle_other_deg1.5981.5724437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.25522.083120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64815331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4991513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022477
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
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_it0.6431.0661045
X-RAY DIFFRACTIONr_mcbond_other0.6361.0651044
X-RAY DIFFRACTIONr_mcangle_it0.9731.5971308
X-RAY DIFFRACTIONr_mcangle_other0.9741.5981309
X-RAY DIFFRACTIONr_scbond_it1.2851.2331154
X-RAY DIFFRACTIONr_scbond_other1.2851.2331155
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9591.8011698
X-RAY DIFFRACTIONr_long_range_B_refined4.07213.7112699
X-RAY DIFFRACTIONr_long_range_B_other3.92813.2092650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 132 -
Rwork0.285 2503 -
obs--97.52 %
Refinement TLS params.Method: refined / Origin x: 34.2923 Å / Origin y: 14.2465 Å / Origin z: 20.0263 Å
111213212223313233
T0.0214 Å2-0.0019 Å2-0.0049 Å2-0.0057 Å20.0028 Å2--0.0094 Å2
L1.0722 °2-0.147 °20.1379 °2-0.4395 °20.0967 °2--0.7038 °2
S-0.0234 Å °-0.0234 Å °-0.0291 Å °0.0206 Å °0.0243 Å °-0.0144 Å °0.022 Å °0.0455 Å °-0.0009 Å °

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