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- PDB-5lgc: T48 deacetylase with substrate -

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Basic information

Entry
Database: PDB / ID: 5lgc
TitleT48 deacetylase with substrate
ComponentsArCE4A
KeywordsHYDROLASE / deacetylase
Function / homologyGlycoside hydrolase/deacetylase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesArthrobacter sp. AW19M34-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsRothweiler, U.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norway
CitationJournal: PLoS ONE / Year: 2017
Title: Structure and function of a CE4 deacetylase isolated from a marine environment.
Authors: Tuveng, T.R. / Rothweiler, U. / Udatha, G. / Vaaje-Kolstad, G. / Smalas, A. / Eijsink, V.G.H.
History
DepositionJul 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Structure summary / Category: entity / Item: _entity.details / _entity.pdbx_description
Revision 1.2Nov 1, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: ArCE4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4532
Polymers25,0281
Non-polymers4241
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-5 kcal/mol
Surface area8970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.490, 56.410, 82.420
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 ArCE4A


Mass: 25028.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DNA sequence deposited at http://www.ebi.ac.uk/ena/data/view/LT630322
Source: (gene. exp.) Arthrobacter sp. AW19M34-1 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES pH 6.5 15-30% PEG (1.5K; 2K; 3350 or 4K)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2015 / Details: Toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 11021 / % possible obs: 93.9 % / Redundancy: 4.5 % / CC1/2: 0.999 / Net I/σ(I): 17.96
Reflection shellResolution: 2.09→2.21 Å / Redundancy: 4 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.69 / CC1/2: 0.936 / % possible all: 71.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LFZ

5lfz


Resolution: 2.09→36.341 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.18
RfactorNum. reflection% reflection
Rfree0.2225 567 5.15 %
Rwork0.1847 --
obs0.1868 11015 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→36.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 29 40 1627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061630
X-RAY DIFFRACTIONf_angle_d0.932225
X-RAY DIFFRACTIONf_dihedral_angle_d14.889594
X-RAY DIFFRACTIONf_chiral_restr0.037257
X-RAY DIFFRACTIONf_plane_restr0.004284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0886-2.29870.29891080.20872179X-RAY DIFFRACTION80
2.2987-2.63130.25681310.21472719X-RAY DIFFRACTION99
2.6313-3.31480.23631620.20382714X-RAY DIFFRACTION99
3.3148-36.34690.19981660.16562836X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 11.2094 Å / Origin y: -3.4553 Å / Origin z: -14.5284 Å
111213212223313233
T0.1409 Å2-0.0068 Å20.0162 Å2-0.2282 Å20.0252 Å2--0.2637 Å2
L2.7145 °20.6097 °20.2756 °2-2.9798 °21.2516 °2--2.7399 °2
S0.0221 Å °-0.0998 Å °-0.2167 Å °0.0463 Å °0.0377 Å °-0.1396 Å °-0.0357 Å °0.1572 Å °-0.0413 Å °
Refinement TLS groupSelection details: (chain A and resseq 18:216)

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