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- PDB-5lfz: T48 deacetylase -

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Basic information

Entry
Database: PDB / ID: 5lfz
TitleT48 deacetylase
ComponentsArCE4A
KeywordsHYDROLASE / deacetylase
Function / homologyGlycoside hydrolase/deacetylase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / NICKEL (II) ION
Function and homology information
Biological speciesArthrobacter sp. AW19M34-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 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 5, 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: Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
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_shell
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)25,0872
Polymers25,0281
Non-polymers591
Water1,928107
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-12 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.090, 56.770, 76.860
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) / Gene: AA310_02990, ATC04_16800 / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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 % sol: 27.8 %
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: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 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: 1.56→35 Å / Num. obs: 25036 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c1g

2c1g


Resolution: 1.561→34.843 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.9
RfactorNum. reflection% reflection
Rfree0.2051 1883 8.05 %
Rwork0.1785 --
obs0.1806 23405 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.561→34.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 1 107 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051647
X-RAY DIFFRACTIONf_angle_d0.9572243
X-RAY DIFFRACTIONf_dihedral_angle_d13.45603
X-RAY DIFFRACTIONf_chiral_restr0.038251
X-RAY DIFFRACTIONf_plane_restr0.004289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5613-1.60350.45281200.37051269X-RAY DIFFRACTION75
1.6035-1.65070.33911290.31441466X-RAY DIFFRACTION85
1.6507-1.7040.28791330.26431510X-RAY DIFFRACTION87
1.704-1.76490.2591330.24721577X-RAY DIFFRACTION90
1.7649-1.83550.26611360.22591591X-RAY DIFFRACTION92
1.8355-1.91910.23391460.19971673X-RAY DIFFRACTION96
1.9191-2.02020.22071490.18651708X-RAY DIFFRACTION98
2.0202-2.14680.21941530.16821733X-RAY DIFFRACTION99
2.1468-2.31250.21091520.16461747X-RAY DIFFRACTION99
2.3125-2.54520.21171530.16841763X-RAY DIFFRACTION100
2.5452-2.91330.21751560.18331778X-RAY DIFFRACTION100
2.9133-3.66980.20991580.16891811X-RAY DIFFRACTION100
3.6698-34.85130.15891650.16131896X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2708-0.58120.40250.6362-0.69021.99710.12510.06940.1463-0.0715-0.2023-0.1047-0.13730.27320.00010.2366-0.03620.00780.2340.00750.24534.591337.321422.8758
21.4685-0.0082-0.28010.8438-0.3442.3209-0.0395-0.2646-0.02020.12380.02120.06150.1747-0.1313-0.00010.2598-0.0453-0.00170.26760.00950.244126.160926.811333.6694
31.2124-0.3672-0.15441.08950.00711.32140.02560.1821-0.021-0.1576-0.06580.07450.0131-0.1679-0.00020.23-0.005-0.01060.2148-0.0140.224324.608335.912717.7459
41.05990.24390.68921.1525-0.85751.3773-0.0311-0.04540.16520.118-0.10430.0247-0.26450.1220.00020.2751-0.0178-0.00360.2093-0.03620.265428.994442.630323.5654
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 133 )
3X-RAY DIFFRACTION3chain 'A' and (resid 134 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 218 )

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