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- PDB-2fs5: Crystal structure of TDP-fucosamine acetyltransferase (WecD)- apo form -

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Basic information

Entry
Database: PDB / ID: 2fs5
TitleCrystal structure of TDP-fucosamine acetyltransferase (WecD)- apo form
ComponentsTDP-Fucosamine acetyltransferase
KeywordsTRANSFERASE / GNAT fold / acetyltransferase / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase / enterobacterial common antigen biosynthetic process / N-acetyltransferase activity
Similarity search - Function
dTDP-fucosamine acetyltransferase WecD / : / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / Ankyrin repeat / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
dTDP-fucosamine acetyltransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsHung, M.N. / Rangarajan, E. / Munger, C. / Nadeau, G. / Sulea, T. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Bacteriol. / Year: 2006
Title: Crystal Structure of TDP-Fucosamine Acetyltransferase (WecD) from Escherichia coli, an Enzyme Required for Enterobacterial Common Antigen Synthesis.
Authors: Hung, M.N. / Rangarajan, E. / Munger, C. / Nadeau, G. / Sulea, T. / Matte, A.
History
DepositionJan 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TDP-Fucosamine acetyltransferase
B: TDP-Fucosamine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9523
Polymers50,8872
Non-polymers651
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-39 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.837, 84.837, 155.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein TDP-Fucosamine acetyltransferase


Mass: 25443.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: wecd / Plasmid: pFO4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8FBQ3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM sodium acetate, 10 mM zinc sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X8C11.1
SYNCHROTRONNSLS X8C21.282, 1.283
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDNov 7, 2004monochromator
ADSC QUANTUM 42CCDNov 7, 2004monochromator
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.2821
31.2831
ReflectionResolution: 1.95→32.8 Å / Num. obs: 40825 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.95→32.8 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.132 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 2012 5 %RANDOM
Rwork0.18136 ---
obs0.18343 38592 96.19 %-
all-38592 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 1 628 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223458
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.9274714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.42323.038158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80715524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3631534
X-RAY DIFFRACTIONr_chiral_restr0.0990.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022680
X-RAY DIFFRACTIONr_nbd_refined0.2010.21632
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2482
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.251
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1280.21
X-RAY DIFFRACTIONr_mcbond_it1.1081.52260
X-RAY DIFFRACTIONr_mcangle_it1.46323500
X-RAY DIFFRACTIONr_scbond_it2.47531397
X-RAY DIFFRACTIONr_scangle_it3.4944.51214
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 137 -
Rwork0.201 2924 -
obs--99.64 %

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