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- PDB-6uar: Crystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase... -

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Basic information

Entry
Database: PDB / ID: 6uar
TitleCrystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I) in complex with laminaritriose
ComponentsGlyco_hydro_cc domain-containing protein
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyUncharacterised 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 speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCosta, P.A.C.R. / Santos, C.R. / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)28,4222
Polymers27,9181
Non-polymers5041
Water5,495305
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)37.758, 77.980, 46.228
Angle α, β, γ (deg.)90.000, 102.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 27917.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G0FQ07
#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5]/1-1-1/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 8% PEG20000 8% PEGMME 550 0.1 M sodium acetate 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.23985 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.4→45.15 Å / Num. obs: 48504 / % possible obs: 94.7 % / Redundancy: 4.62 % / CC1/2: 0.999 / Net I/σ(I): 15.73
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 7301 / CC1/2: 0.672

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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: 1.4→36.9 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 2335 4.8 %RANDOM
Rwork0.1692 ---
obs0.1698 46173 94.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.49 Å2 / Biso mean: 18.638 Å2 / Biso min: 8.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å2-0 Å20.42 Å2
2---0.33 Å20 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.4→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 34 305 2152
Biso mean--31.19 35.4 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131940
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171709
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.6742660
X-RAY DIFFRACTIONr_angle_other_deg2.4161.5923943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1445243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41620.5198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80115262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3891515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022211
X-RAY DIFFRACTIONr_gen_planes_other0.0240.02458
X-RAY DIFFRACTIONr_mcbond_it2.3231.697968
X-RAY DIFFRACTIONr_mcbond_other2.2891.692966
X-RAY DIFFRACTIONr_mcangle_it3.1512.5611209
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 146 -
Rwork0.311 3228 -
all-3374 -
obs--89.66 %

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