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

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Basic information

Entry
Database: PDB / ID: 6ufl
TitleCrystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) from Amycolatopsis mediterranei (AmGH128_I) in the complex with laminarihexaose
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 / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsCordeiro, R.L. / Domingues, M.N. / Vieira, P.S. / 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 24, 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)28,9082
Polymers27,9171
Non-polymers9911
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.096, 77.757, 46.481
Angle α, β, γ (deg.)90.00, 101.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 27916.943 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-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-3DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a2122h-1b_1-5]/1-1-1-1-1-1/a3-b1_b3-c1_c3-d1_d3-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][b-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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) Polyethylene glycol 3.350, 0.2 M Potassium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 32212 / % possible obs: 94 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 9.3
Reflection shellResolution: 1.61→1.71 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4967 / CC1/2: 0.835 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.227 1611 5.001 %
Rwork0.187 --
obs-32211 94 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å21.319 Å2
2---0.515 Å20 Å2
3----0.528 Å2
Refinement stepCycle: LAST / Resolution: 1.61→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 67 262 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131961
X-RAY DIFFRACTIONr_bond_other_d0.0360.0171719
X-RAY DIFFRACTIONr_angle_refined_deg2.0631.6992693
X-RAY DIFFRACTIONr_angle_other_deg3.2111.6173959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2085246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.31520.53294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97515252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6561514
X-RAY DIFFRACTIONr_chiral_restr0.110.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.022217
X-RAY DIFFRACTIONr_gen_planes_other0.0330.02457
X-RAY DIFFRACTIONr_nbd_refined0.2060.2405
X-RAY DIFFRACTIONr_nbd_other0.240.239
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2980
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2198
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_it1.4442.09975
X-RAY DIFFRACTIONr_mcbond_other1.3592.082973
X-RAY DIFFRACTIONr_mcangle_it2.1633.1271221
X-RAY DIFFRACTIONr_mcangle_other2.1353.1261221
X-RAY DIFFRACTIONr_scbond_it1.8452.201986
X-RAY DIFFRACTIONr_scbond_other1.8442.201987
X-RAY DIFFRACTIONr_scangle_it2.7183.2541471
X-RAY DIFFRACTIONr_scangle_other2.7833.2521472
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.611-1.6530.2691090.25620630.25725330.8130.82185.74810.24
1.653-1.6980.2331140.23121770.23124480.870.86793.58660.21
1.698-1.7470.2621120.2221290.22223840.8680.87994.00170.193
1.747-1.8010.2641110.21520950.21823380.8510.88794.35410.187
1.801-1.860.271060.21220230.21522430.8850.89994.91750.179
1.86-1.9250.2611050.21119900.21422010.8910.90995.1840.18
1.925-1.9980.255980.19318750.19620790.9090.92194.90140.166
1.998-2.0790.202970.19318380.19420190.940.93495.83950.168
2.079-2.1710.255920.19917500.20119310.8980.92295.3910.175
2.171-2.2770.252900.19816950.20118750.9160.92295.20.176
2.277-2.40.215820.17215760.17417500.9460.9594.74290.153
2.4-2.5450.233810.17815400.18117170.9340.94594.40890.161
2.545-2.720.224740.18513880.18715530.9120.93994.14040.174
2.72-2.9370.25690.18813160.19114690.9180.9494.28180.184
2.937-3.2160.219630.1911980.19113500.9280.9493.40740.187
3.216-3.5940.231590.17911170.18212270.9420.96295.84350.189
3.594-4.1450.232520.1619870.16510880.9480.96195.49630.175
4.145-5.0660.125430.1568270.1549170.9780.9794.87460.183
5.066-7.1210.233340.1746450.1777120.9470.9595.36520.201
7.121-45.4670.246200.1813700.1844240.9380.94691.98110.208

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