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- PDB-5zgn: The crystal structure of KacTA-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5zgn
TitleThe crystal structure of KacTA-DNA complex
Components
  • (DNA (27-MER)) x 2
  • KacA
  • KacT
KeywordsTOXIN / KacT / KacA / Complex
Function / homology
Function and homology information


N-acetyltransferase activity / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
DNA / DNA (> 10) / Uncharacterized protein / Putative GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsQian, H.L. / Yao, Q.Q. / Gan, J.H. / Ou, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology2015CB554202 China
CitationJournal: To Be Published
Title: The crystal structure of KacTA-DNA complex
Authors: Qian, H.L. / Yao, Q.Q. / Gan, J.H. / Ou, H.Y.
History
DepositionMar 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KacA
B: KacA
C: KacT
D: KacA
E: KacA
F: KacT
G: DNA (27-MER)
H: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67211
Polymers97,3848
Non-polymers2883
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-208 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.046, 62.044, 61.994
Angle α, β, γ (deg.)93.83, 93.99, 93.93
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 6 molecules ABDECF

#1: Protein
KacA


Mass: 10152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: KacA
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_05880
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: A0A0H3GLZ1
#2: Protein KacT


Mass: 20093.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_05890
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: A0A0H3GMP0

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DNA chain , 2 types, 2 molecules GH

#3: DNA chain DNA (27-MER)


Mass: 8323.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (27-MER)


Mass: 8265.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 54 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.24 Å3/Da / Density % sol: 45.06 % / Description: rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 38226 / % possible obs: 94.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.4
Reflection shellResolution: 2.24→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.311 / % possible all: 92.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→28.44 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 28.35
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.255 1862 4.87 %
Rwork0.214 --
obs0.216 38196 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 1101 15 51 6018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046183
X-RAY DIFFRACTIONf_angle_d0.8328592
X-RAY DIFFRACTIONf_dihedral_angle_d22.353547
X-RAY DIFFRACTIONf_chiral_restr0.068984
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2369-2.29740.34141350.31192641X-RAY DIFFRACTION88
2.2974-2.3650.33481510.29852734X-RAY DIFFRACTION93
2.365-2.44130.30471560.28962706X-RAY DIFFRACTION92
2.4413-2.52850.30961400.27792651X-RAY DIFFRACTION89
2.5285-2.62960.30591740.2652829X-RAY DIFFRACTION95
2.6296-2.74920.2761250.26692842X-RAY DIFFRACTION95
2.7492-2.8940.25391530.25492858X-RAY DIFFRACTION95
2.894-3.07510.30791390.25232821X-RAY DIFFRACTION95
3.0751-3.31220.29041690.25032737X-RAY DIFFRACTION92
3.3122-3.6450.30591620.22012922X-RAY DIFFRACTION98
3.645-4.1710.2461330.19532888X-RAY DIFFRACTION97
4.171-5.24960.18921150.18292833X-RAY DIFFRACTION94
5.2496-28.43770.23331100.18142872X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 56.1852 Å / Origin y: -10.6855 Å / Origin z: 65.3312 Å
111213212223313233
T0.2993 Å2-0.0402 Å2-0.0244 Å2-0.3885 Å2-0.09 Å2--0.3821 Å2
L1.2619 °2-0.3532 °2-0.4128 °2-0.5873 °2-0.0112 °2--0.5007 °2
S0.0559 Å °-0.0005 Å °0.0047 Å °0.0055 Å °-0.0247 Å °-0.0188 Å °-0.0093 Å °-0.033 Å °-0.0409 Å °
Refinement TLS groupSelection details: ALL

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