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

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Basic information

Entry
Database: PDB / ID: 6uaq
TitleCrystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase from Amycolatopsis mediterranei (AmGH128_I)
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 / MIRAS / Resolution: 1.15 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 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
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)28,2175
Polymers27,9181
Non-polymers2994
Water6,395355
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)37.350, 78.643, 46.183
Angle α, β, γ (deg.)90.000, 101.620, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.59 Å3/Da / Density % sol: 52.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: sodium acetate 0.1 M sodium chloride 1.5 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.03314 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 1.15→45.28 Å / Num. obs: 171671 / % possible obs: 94 % / Redundancy: 2.35 % / CC1/2: 0.998 / Net I/σ(I): 11.51
Reflection shellResolution: 1.15→1.22 Å / Num. unique obs: 24853 / CC1/2: 0.808

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 1.15→45.28 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 4403 4.8 %RANDOM
Rwork0.15 ---
obs0.1506 86795 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 97.21 Å2 / Biso mean: 12.728 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20.42 Å2
2---0.58 Å2-0 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 1.15→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 19 355 2187
Biso mean--21.68 28.94 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0121936
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171722
X-RAY DIFFRACTIONr_angle_refined_deg2.0971.6482645
X-RAY DIFFRACTIONr_angle_other_deg2.441.5673976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.985241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69420.396101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27915270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9251516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022214
X-RAY DIFFRACTIONr_gen_planes_other0.0220.02462
X-RAY DIFFRACTIONr_mcbond_it3.6681.127966
X-RAY DIFFRACTIONr_mcbond_other3.2511.118964
X-RAY DIFFRACTIONr_mcangle_it4.2211.6881206
LS refinement shellResolution: 1.151→1.181 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 314 -
Rwork0.241 6304 -
all-6618 -
obs--96.77 %

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