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- PDB-4whn: Structure of toxin-activating acyltransferase (TAAT) -

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Basic information

Entry
Database: PDB / ID: 4whn
TitleStructure of toxin-activating acyltransferase (TAAT)
ComponentsApxC
KeywordsTRANSFERASE / TAAT / GNAT / Toxin-activating acyltransferase / ACP binding
Function / homologyRTX toxin-activating protein C, bacteria / RTX toxin acyltransferase family / toxin metabolic process / hemolysis in another organism / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm / CITRIC ACID / RTX-I toxin-activating lysine-acyltransferase ApxIC
Function and homology information
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsCrow, A. / Greene, N.P. / Hughes, C. / Koronakis, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of a bacterial toxin-activating acyltransferase.
Authors: Greene, N.P. / Crow, A. / Hughes, C. / Koronakis, V.
History
DepositionSep 23, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jun 17, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ApxC
B: ApxC
C: ApxC
D: ApxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9735
Polymers84,7814
Non-polymers1921
Water3,945219
1
A: ApxC
C: ApxC


Theoretical massNumber of molelcules
Total (without water)42,3902
Polymers42,3902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-20 kcal/mol
Surface area19050 Å2
MethodPISA
2
B: ApxC
D: ApxC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5823
Polymers42,3902
Non-polymers1921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-17 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.450, 86.370, 131.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA4 - 17015 - 181
21VALVALBB4 - 17015 - 181
12VALVALAA4 - 17015 - 181
22VALVALCC4 - 17015 - 181
13VALVALAA4 - 17015 - 181
23VALVALDD4 - 17015 - 181
14VALVALBB4 - 17015 - 181
24VALVALCC4 - 17015 - 181
15VALVALBB4 - 17015 - 181
25VALVALDD4 - 17015 - 181
16ASNASNCC4 - 17115 - 182
26ASNASNDD4 - 17115 - 182

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ApxC / APX-IC / Cytolysin IC / CLY-IC / HLY-IC / RTX-I toxin determinant C / Toxin RTX-I-activating ...APX-IC / Cytolysin IC / CLY-IC / HLY-IC / RTX-I toxin determinant C / Toxin RTX-I-activating protein C / RTX-I toxin-activating lysine-acyltransferase ApxIC


Mass: 21195.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Gene: apxIC, clyIC, hlyIC / Production host: Escherichia coli (E. coli)
References: UniProt: P55132, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: Crystallisation reagent is 32% PEG300, Phosphate-citrate buffer, pH 4.4. Protein solution is 5 mg/ml ApxC in 150mM NaCl, 20 mM HEPES pH 7.5. Sitting drops formed by 2 ul Protein solution and ...Details: Crystallisation reagent is 32% PEG300, Phosphate-citrate buffer, pH 4.4. Protein solution is 5 mg/ml ApxC in 150mM NaCl, 20 mM HEPES pH 7.5. Sitting drops formed by 2 ul Protein solution and 1 ul crystallisation reagent equilibrated over 80 ul of the reagent alone.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.15→54.29 Å / Num. obs: 51711 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.104 / Net I/σ(I): 12.6
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.804 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→54.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.424 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24238 2629 5.1 %RANDOM
Rwork0.20018 ---
obs0.20228 49014 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.981 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.38 Å20 Å2
3----2.66 Å2
Refinement stepCycle: 1 / Resolution: 2.15→54.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5541 0 13 219 5773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195820
X-RAY DIFFRACTIONr_bond_other_d0.010.025492
X-RAY DIFFRACTIONr_angle_refined_deg1.7141.9347900
X-RAY DIFFRACTIONr_angle_other_deg1.652312625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83924.089291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9615993
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4151532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216634
X-RAY DIFFRACTIONr_gen_planes_other0.010.021458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.493.7112756
X-RAY DIFFRACTIONr_mcbond_other3.4873.7092755
X-RAY DIFFRACTIONr_mcangle_it5.1075.5393459
X-RAY DIFFRACTIONr_mcangle_other5.1085.5423460
X-RAY DIFFRACTIONr_scbond_it4.0474.1113064
X-RAY DIFFRACTIONr_scbond_other4.0354.113062
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1575.9714441
X-RAY DIFFRACTIONr_long_range_B_refined8.17229.9456865
X-RAY DIFFRACTIONr_long_range_B_other8.16629.926809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95270.14
12B95270.14
21A92590.15
22C92590.15
31A92600.15
32D92600.15
41B91210.16
42C91210.16
51B91840.16
52D91840.16
61C98090.11
62D98090.11
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 210 -
Rwork0.277 3537 -
obs--99.87 %

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