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- PDB-3i3g: Crystal Structure of Trypanosoma brucei N-acetyltransferase (Tb11... -

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Basic information

Entry
Database: PDB / ID: 3i3g
TitleCrystal Structure of Trypanosoma brucei N-acetyltransferase (Tb11.01.2886) at 1.86A
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / Trypanosoma brucei / malaria / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


glucosamine-phosphate N-acetyltransferase / glucosamine 6-phosphate N-acetyltransferase activity / N-acetylglucosamine metabolic process / UDP-N-acetylglucosamine biosynthetic process / glycosome / monosaccharide binding / endoplasmic reticulum-Golgi intermediate compartment / Golgi apparatus / endoplasmic reticulum
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / 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
Glucosamine 6-phosphate N-acetyltransferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsQiu, W. / Wernimont, A.K. / Marino, K. / Zhang, A.Z. / Ma, D. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. ...Qiu, W. / Wernimont, A.K. / Marino, K. / Zhang, A.Z. / Ma, D. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / J Ferguson, M.A. / Hui, R. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure Trypanosoma brucei N-acetyltransferase (Tb11.01.2886) at 1.86A
Authors: Qiu, W. / Wernimont, A.K. / Marino, K. / Zhang, A.Z. / Ma, D. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / ...Authors: Qiu, W. / Wernimont, A.K. / Marino, K. / Zhang, A.Z. / Ma, D. / Lin, Y.H. / Mackenzie, F. / Kozieradzki, I. / Cossar, D. / Zhao, Y. / Schapira, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Edwards, A.M. / J Ferguson, M.A. / Hui, R. / Structural Genomics Consortium
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase
B: N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)36,0212
Polymers36,0212
Non-polymers00
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-28 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.860, 64.440, 82.770
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

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Components

#1: Protein N-acetyltransferase /


Mass: 18010.709 Da / Num. of mol.: 2 / Fragment: Residues 5-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: Tb11.01.2886 / Production host: Escherichia coli (E. coli) / References: UniProt: Q383G8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 62 HAS BEEN CONFIRMED TO BE ARG NOT ONLY BY THE ELECTRON DENSITY, AS SEEN ...THE RESIDUE AT POSITION 62 HAS BEEN CONFIRMED TO BE ARG NOT ONLY BY THE ELECTRON DENSITY, AS SEEN IN THE FINAL MODEL, BUT ALSO WITH MASS SPECTROMETRY DATA

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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: 1.88 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 19% PEG3350, 0.2M (NH4)2Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→35.96 Å / Num. all: 23634 / Num. obs: 23625 / % possible obs: 99.962 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 20.24 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 25.5
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 7.5 / Num. unique all: 3388 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FB3

3fb3


Resolution: 1.86→35.96 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.882 / SU B: 4.199 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 1217 5.2 %RANDOM
Rwork0.24344 ---
all0.245 23625 --
obs0.2454 22408 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.86→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 0 238 2503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0222301
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5311.9953110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5685302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9522.26897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64315434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9691525
X-RAY DIFFRACTIONr_chiral_restr0.040.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0211711
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.2041.51443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38922328
X-RAY DIFFRACTIONr_scbond_it0.523858
X-RAY DIFFRACTIONr_scangle_it0.9074.5773
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1061 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.590.5
Bmedium thermal0.132
LS refinement shellResolution: 1.86→1.906 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 95 -
Rwork0.309 1628 -
obs--99.77 %

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