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- PDB-6ubd: Crystal structure of a GH128 (subgroup VII) oligosaccharide-bindi... -

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Basic information

Entry
Database: PDB / ID: 6ubd
TitleCrystal structure of a GH128 (subgroup VII) oligosaccharide-binding protein from Trichoderma gamsii (TgGH128_VII)
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 / fungal-type cell wall / Glycoside hydrolase superfamily / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesTrichoderma gamsii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSantos, C.R. / Costa, P.A.C.R. / Souza, B.P. / 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 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)30,7251
Polymers30,7251
Non-polymers00
Water9,098505
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)67.345, 74.088, 50.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-544-

HOH

21A-693-

HOH

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 30724.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma gamsii (fungus) / Gene: TGAM01_v206169, TGAMA5MH_01007 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0W7VXC1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MES 0.1 M 20% PEG6000 Lithium chloride 0.2 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.99996 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99996 Å / Relative weight: 1
ReflectionResolution: 1.25→41.94 Å / Num. obs: 69710 / % possible obs: 98 % / Redundancy: 6.41 % / CC1/2: 0.997 / Net I/σ(I): 11.12
Reflection shellResolution: 1.25→1.33 Å / Num. unique obs: 10928 / CC1/2: 0.822

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→41.94 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 3478 5 %RANDOM
Rwork0.1689 ---
obs0.1698 66294 98.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.04 Å2 / Biso mean: 11.724 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å2-0 Å2
2--1.48 Å2-0 Å2
3----1.31 Å2
Refinement stepCycle: final / Resolution: 1.25→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 0 505 2518
Biso mean---25.72 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132115
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171780
X-RAY DIFFRACTIONr_angle_refined_deg2.0381.6292895
X-RAY DIFFRACTIONr_angle_other_deg2.4831.5724178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7915260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51125.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.9215320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.049154
X-RAY DIFFRACTIONr_chiral_restr0.1190.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022411
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02437
X-RAY DIFFRACTIONr_mcbond_it1.2790.9471031
X-RAY DIFFRACTIONr_mcbond_other1.2790.9461030
X-RAY DIFFRACTIONr_mcangle_it1.7251.4291288
LS refinement shellResolution: 1.249→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 260 -
Rwork0.394 4746 -
all-5006 -
obs--96.27 %

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