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- PDB-6wqb: Crystal structure of VipF from Legionella hackeliae in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6wqb
TitleCrystal structure of VipF from Legionella hackeliae in complex with acetyl-CoA
ComponentsN-terminal acetyltransferase, GNAT familyPeptide alpha-N-acetyltransferase
KeywordsTRANSFERASE / acetyltransferase / acetyl coenzyme A / acetyl CoA / legionella hackeliae / legionella pneumophila / effector / VipF
Function / homologyAcetyltransferase (GNAT) family / acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / N-terminal acetyltransferase, GNAT family
Function and homology information
Biological speciesLegionella hackeliae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsStogios, P.J. / Skarina, T. / Wawrzak, Z. / Sandoval, J. / Di Leo, R. / Savchenko, A.
CitationJournal: To Be Published
Title: Crystal structure of VipF from Legionella hackeliae in complex with acetyl-CoA
Authors: Stogios, P.J.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-terminal acetyltransferase, GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2683
Polymers33,6491
Non-polymers1,6192
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.586, 36.427, 59.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein N-terminal acetyltransferase, GNAT family / Peptide alpha-N-acetyltransferase / VipF


Mass: 33649.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella hackeliae (bacteria) / Gene: vipF, LHA_0223 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A0A8UKD4
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) PEG3350, 0.2 M calcium chloride, 5 mM acetyl-CoA, Cryoprotectant: paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 38174 / % possible obs: 99.9 % / Redundancy: 4.9 % / Biso Wilson estimate: 24.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Net I/σ(I): 30.54
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1866 / CC1/2: 0.763 / Rpim(I) all: 0.382 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WQC

6wqc


Resolution: 1.75→29.67 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6521
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1904 5 %RANDOM
Rwork0.1836 ---
obs0.1852 38109 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 102 274 2717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02192514
X-RAY DIFFRACTIONf_angle_d1.6683434
X-RAY DIFFRACTIONf_chiral_restr0.1051372
X-RAY DIFFRACTIONf_plane_restr0.0101431
X-RAY DIFFRACTIONf_dihedral_angle_d18.8036900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.37961110.29552126X-RAY DIFFRACTION83.81
1.79-1.840.26171360.25782587X-RAY DIFFRACTION99.93
1.84-1.890.26421350.23232561X-RAY DIFFRACTION99.89
1.89-1.950.29391350.20712568X-RAY DIFFRACTION99.82
1.95-2.020.20791360.20282595X-RAY DIFFRACTION99.89
2.02-2.10.24621350.20092568X-RAY DIFFRACTION99.96
2.1-2.20.20221370.18462597X-RAY DIFFRACTION99.96
2.2-2.320.25051370.18912609X-RAY DIFFRACTION99.96
2.32-2.460.21061370.19022599X-RAY DIFFRACTION100
2.46-2.650.21271370.19472617X-RAY DIFFRACTION100
2.65-2.920.23361390.1942630X-RAY DIFFRACTION99.93
2.92-3.340.22911400.18512657X-RAY DIFFRACTION99.79
3.34-4.20.181400.15582674X-RAY DIFFRACTION99.86
4.2-29.670.18771490.16632817X-RAY DIFFRACTION99.06
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)
15.20713198344-0.7784444943880.7129341744084.35615265712-0.1992179456162.12428618780.222797868224-0.0399795739388-0.07082928435210.0212719347506-0.0387001619102-0.5604599951010.2021590265350.0785680003265-0.1467792564170.1725393077540.0157755253434-0.01532979618840.150673198619-0.002718617235980.31081310454372.375921032837.487694196642.0981264752
23.518950194090.892025605552-1.311595517331.2947445304-0.2387647812341.851720825080.0394669908780.2607765176180.07774630376720.0477179825952-0.0345956965401-0.0820287213775-0.000315954836479-0.0481035578867-0.02342960969530.1941009561240.0655293977952-0.03079560948770.1998404254670.01239991650740.1085227773748.922777550135.274937099839.4912474303
37.30575787577-4.654865743685.2933961633.61871130459-4.272388645165.53449202875-0.06263355022811.409824585930.915894956904-1.78973952149-0.901362972562-1.315162743730.1215557262530.6673314457980.7304788517630.6828584924720.01290124604610.1707108294140.4689081393860.05117717346230.46295670865647.446629251219.934745046736.5124664583
41.444074365590.188415295406-0.4217216728161.76219730477-0.1756243019911.974474935710.009590455696210.0704168219501-0.005723185294640.0736076911666-0.0871641778005-0.03306500874190.09937745651950.07000027675950.07988696890180.2025904923530.034259819028-0.02797265935320.198976029339-0.0258829322210.087186526115245.655102006333.445192170643.6361289009
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:100)
2X-RAY DIFFRACTION2(chain A and resid 101:168)
3X-RAY DIFFRACTION3(chain A and resid 169:178)
4X-RAY DIFFRACTION4(chain A and resid 179:289)

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