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

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Basic information

Entry
Database: PDB / ID: 6ufz
TitleCrystal structure of a GH128 (subgroup I) endo-beta-1,3-glucanase (E199Q mutant) 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 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 25, 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 1.3Mar 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


Theoretical massNumber of molelcules
Total (without water)27,9171
Polymers27,9171
Non-polymers00
Water2,036113
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)35.877, 75.378, 79.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glyco_hydro_cc domain-containing protein


Mass: 27916.943 Da / Num. of mol.: 1 / Mutation: E199Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G0FQ07
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.0 M sodium chloride, 0.1 M sodium acetate, pH 4.6

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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 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 17237 / % possible obs: 98.2 % / Redundancy: 3.7 % / CC1/2: 0.985 / Net I/σ(I): 5
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2658 / CC1/2: 0.702 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→37.69 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / Cross valid method: FREE R-VALUE / ESU R: 0.194 / ESU R Free: 0.175
Details: HYDROGENS HAVE BEEN ADDED IN THEIR RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.262 862 5.001 %
Rwork0.212 --
obs-17235 98.2 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.918 Å20 Å20 Å2
2---1.072 Å20 Å2
3---1.989 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 113 1906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121861
X-RAY DIFFRACTIONr_bond_other_d0.0370.0171635
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.6452545
X-RAY DIFFRACTIONr_angle_other_deg2.4441.5673766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65320.8693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50615248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5581513
X-RAY DIFFRACTIONr_chiral_restr0.0740.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022166
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02445
X-RAY DIFFRACTIONr_nbd_refined0.1990.2410
X-RAY DIFFRACTIONr_nbd_other0.2620.265
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2922
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2108
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_it1.1472.197955
X-RAY DIFFRACTIONr_mcbond_other1.1482.197953
X-RAY DIFFRACTIONr_mcangle_it1.9053.2851192
X-RAY DIFFRACTIONr_mcangle_other1.9053.2851192
X-RAY DIFFRACTIONr_scbond_it1.2672.315906
X-RAY DIFFRACTIONr_scbond_other1.2672.315906
X-RAY DIFFRACTIONr_scangle_it2.0393.4281353
X-RAY DIFFRACTIONr_scangle_other2.0383.4281353
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
1.901-1.950.315600.34111460.3412600.7640.795.71430.332
1.95-2.0030.532590.38911280.39712420.5330.60495.57170.389
2.003-2.0610.298600.31611260.31512030.6990.62998.58690.297
2.061-2.1240.292580.26811130.26911870.7850.78798.65210.241
2.124-2.1940.276560.23710530.23911230.8580.85598.75330.207
2.194-2.270.293540.21710400.2211060.8050.87998.9150.188
2.27-2.3560.264530.21410040.21710660.90.88399.15570.185
2.356-2.4510.227510.2019590.20210220.9160.998.82580.165
2.451-2.560.324500.1819440.18810070.8720.91998.7090.148
2.56-2.6840.252450.1878710.199300.8950.91198.49460.153
2.684-2.8290.267450.2138430.2169040.8740.90698.23010.18
2.829-2.9990.221420.1778120.1798710.9150.93598.04820.15
2.999-3.2050.223400.1647570.1678050.9410.95299.00620.137
3.205-3.460.233380.1847090.1867540.9260.94699.07160.163
3.46-3.7870.195340.1856630.1867080.9550.95398.44630.17
3.787-4.2280.276320.1755950.186370.9250.95598.43010.161
4.228-4.8720.189290.1555450.1575830.9540.96698.45630.148
4.872-5.9420.218240.1924640.1934950.9570.95198.58590.175
5.942-8.3010.219190.2333720.2323960.9530.94198.73740.214
8.301-37.6890.365130.2512290.2572530.910.94195.65220.269

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