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- PDB-5zmp: The structure of a lysine deacylase -

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Basic information

Entry
Database: PDB / ID: 5zmp
TitleThe structure of a lysine deacylase
Componentslysine deacylase
KeywordsHYDROLASE / lysine deacylase
Function / homology: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / hydrolase activity / metal ion binding / Acetylpolyamine aminohydrolase
Function and homology information
Biological speciesSynechococcus sp. PCC 73109 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsGe, F.
Citation
Journal: To Be Published
Title: The structure of a lysine deacylase
Authors: Ge, F.
#1: Journal: To Be Published
Title: The structure of a lysine deacylase
Authors: Ge, F.
History
DepositionApr 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: lysine deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1562
Polymers34,0911
Non-polymers651
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-38 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.790, 56.790, 112.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein lysine deacylase / Acetylpolyamine aminohydrolase


Mass: 34090.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. PCC 73109 (bacteria) / Gene: SYNPCC7002_A2791 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XMP1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Source detailsProtein used in this structure is derived from Tax ID 374982 (Synechococcus sp. PCC 73109). ...Protein used in this structure is derived from Tax ID 374982 (Synechococcus sp. PCC 73109). Reference source is Tax ID 32049 (Synechococcus sp. PCC 7002). Sequences are 100 % matched.

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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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.26 M Sodium phosphate monobasic monohydrate, 0.14 M Potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→50.7 Å / Num. obs: 18344 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.132 / Net I/σ(I): 8.7
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.13 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1342 / Rpim(I) all: 0.681 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G11

5g11


Resolution: 2.19→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2149 924 5.14 %
Rwork0.1734 --
obs-18344 99.8 %
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 1 222 2614
LS refinement shellResolution: 2.19→2.25 Å /
Rfactor% reflection
Rfree0.173 -
Rwork0.214 -
obs-99.8 %

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