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- PDB-5z6n: Crystal structure of Escherichia coli ElaA -

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Basic information

Entry
Database: PDB / ID: 5z6n
TitleCrystal structure of Escherichia coli ElaA
ComponentsProtein ElaA
KeywordsTRANSFERASE / N-acetyltransferase / acetyl coenzyme A
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShi, L.L. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
CitationJournal: To Be Published
Title: Crystal structure of Escherichia coli ElaA
Authors: Shi, L.L. / Gao, Z.Q. / Zhang, H. / Dong, Y.H.
History
DepositionJan 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 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: Protein ElaA
B: Protein ElaA


Theoretical massNumber of molelcules
Total (without water)34,8752
Polymers34,8752
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-20 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.149, 40.905, 84.648
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein ElaA / acetyltransferase ElaA


Mass: 17437.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: elaA, yfbC, b2267, JW2262 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 0.2M Potassium fluoride, 24%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 14550 / % possible obs: 94.6 % / Redundancy: 5.8 % / CC1/2: 0.983 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.035 / Rrim(I) all: 0.084 / Net I/σ(I): 25.1
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 691 / CC1/2: 0.95 / Rpim(I) all: 0.15 / Rrim(I) all: 0.37 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JPH

5jph


Resolution: 2.6→30.046 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3036 582 5.03 %
Rwork0.2777 --
obs0.2791 11567 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→30.046 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2350 0 0 43 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062410
X-RAY DIFFRACTIONf_angle_d1.0623270
X-RAY DIFFRACTIONf_dihedral_angle_d21.8131425
X-RAY DIFFRACTIONf_chiral_restr0.051359
X-RAY DIFFRACTIONf_plane_restr0.005424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.86160.35521320.31082712X-RAY DIFFRACTION94
2.8616-3.27520.33731520.31022760X-RAY DIFFRACTION95
3.2752-4.12470.38171360.30322517X-RAY DIFFRACTION86
4.1247-30.0480.20891620.2312996X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.6384 Å / Origin y: 3.4762 Å / Origin z: 176.1152 Å
111213212223313233
T0.1973 Å2-0.0245 Å20.0251 Å2-0.1153 Å2-0.0199 Å2--0.1527 Å2
L1.121 °2-0.0946 °20.2184 °2-1.3112 °2-0.2678 °2--2.4852 °2
S-0.0698 Å °-0.0332 Å °0.126 Å °0.248 Å °-0.1228 Å °0.0272 Å °0.2364 Å °0.1141 Å °0.17 Å °
Refinement TLS groupSelection details: all

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