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

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Basic information

Entry
Database: PDB / ID: 6uas
TitleCrystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199A mutant) from Amycolatopsis mediterranei (AmGH128_I) in complex with laminaripentaose
ComponentsGlycoside Hydrolase
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyUncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / beta-D-glucopyranose / DI(HYDROXYETHYL)ETHER / Asl1-like glycosyl hydrolase catalytic domain-containing protein
Function and homology information
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsVieira, P.S. / Cabral, L. / Costa, 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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Glycoside Hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0405
Polymers27,8601
Non-polymers1,1804
Water3,927218
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)36.680, 79.347, 46.152
Angle α, β, γ (deg.)90.000, 103.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glycoside Hydrolase


Mass: 27859.893 Da / Num. of mol.: 1 / Mutation: E199A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G0FQ07

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2-2/a3-b1_b3-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{[(3+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 220 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Zinc Chloride 0.01 M PEG 6000 20% Sodium acetate 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: 1.45856 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45856 Å / Relative weight: 1
ReflectionResolution: 1.91→44.95 Å / Num. obs: 18627 / % possible obs: 92.9 % / Redundancy: 3.89 % / CC1/2: 0.999 / Net I/σ(I): 13.89
Reflection shellResolution: 1.91→2.03 Å / Num. unique obs: 2597 / CC1/2: 0.834

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UAQ

6uaq


Resolution: 1.91→39.14 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.884 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 919 4.9 %RANDOM
Rwork0.1574 ---
obs0.1593 17707 92.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.68 Å2 / Biso mean: 21.95 Å2 / Biso min: 7.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å2-0 Å20.68 Å2
2---1.57 Å2-0 Å2
3---0.46 Å2
Refinement stepCycle: final / Resolution: 1.91→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 76 218 2103
Biso mean--33.99 33.26 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131949
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171716
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.6992670
X-RAY DIFFRACTIONr_angle_other_deg1.4641.6163951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4195242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71920.4393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1115248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.331514
X-RAY DIFFRACTIONr_chiral_restr0.0920.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
LS refinement shellResolution: 1.91→1.959 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.361 47 -
Rwork0.387 1003 -
obs--72.21 %
Refinement TLS params.Method: refined / Origin x: 14.2704 Å / Origin y: -0.1953 Å / Origin z: 0.0563 Å
111213212223313233
T0.0272 Å2-0.0051 Å20.0009 Å2-0.0044 Å2-0.011 Å2--0.0366 Å2
L0.3906 °2-0.1928 °20.0868 °2-0.5261 °2-0.3738 °2--0.7403 °2
S0.0088 Å °0.0004 Å °0.0035 Å °0.0005 Å °0.0052 Å °0.0075 Å °0.0156 Å °-0.0024 Å °-0.0141 Å °

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