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- PDB-4mzu: Crystal structure of FdtD, a bifunctional ketoisomerase/N-acetylt... -

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Basic information

Entry
Database: PDB / ID: 4mzu
TitleCrystal structure of FdtD, a bifunctional ketoisomerase/N-acetyltransferase from Shewanella denitrificans
ComponentsWxcM-like protein
KeywordsISOMERASE / TRANSFERASE / beta-helix / cupin / ketoisomerase / N-acetyltransferase / Acetyl-coenzyme A / dTDP-Fuc3N / dTDP-4-keto-6-deoxyglucose
Function / homology
Function and homology information


acyltransferase activity / metal ion binding
Similarity search - Function
Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) ...Sugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COENZYME A / THYMINE / THYMIDINE-5'-DIPHOSPHATE / WxcM-like protein
Similarity search - Component
Biological speciesShewanella denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChantigian, D.P. / Thoden, J.B. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Biochemical Characterization of a Bifunctional Ketoisomerase/N-Acetyltransferase from Shewanella denitrificans.
Authors: Chantigian, D.P. / Thoden, J.B. / Holden, H.M.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Feb 28, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WxcM-like protein
B: WxcM-like protein
C: WxcM-like protein
D: WxcM-like protein
E: WxcM-like protein
F: WxcM-like protein
G: WxcM-like protein
H: WxcM-like protein
I: WxcM-like protein
J: WxcM-like protein
K: WxcM-like protein
L: WxcM-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)433,46550
Polymers418,17212
Non-polymers15,29338
Water15,259847
1
A: WxcM-like protein
B: WxcM-like protein
C: WxcM-like protein
D: WxcM-like protein
E: WxcM-like protein
F: WxcM-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,93427
Polymers209,0866
Non-polymers7,84821
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33120 Å2
ΔGint-138 kcal/mol
Surface area65510 Å2
MethodPISA
2
G: WxcM-like protein
H: WxcM-like protein
I: WxcM-like protein
J: WxcM-like protein
K: WxcM-like protein
L: WxcM-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,53123
Polymers209,0866
Non-polymers7,44517
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29610 Å2
ΔGint-144 kcal/mol
Surface area65030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.314, 109.443, 127.847
Angle α, β, γ (deg.)79.23, 79.98, 84.89
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
WxcM-like protein


Mass: 34847.625 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans (bacteria) / Strain: OS217 / Gene: FdtD, Sden_2659 / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Roseta2(DE3) / References: UniProt: Q12KT8

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Non-polymers , 5 types, 885 molecules

#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#4: Chemical
ChemComp-TDR / THYMINE


Mass: 126.113 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C5H6N2O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM HEPPS, 7-12% PEG-8000, 100 mM MgCl2, 10 mM dTDP, 10 mM CoA, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2012 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 205722 / Num. obs: 205772 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 27
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 4.7 / Num. unique all: 19668 / Rsym value: 0.223 / % possible all: 87

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model from SAD experiment

Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.622 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.278 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26985 10284 5 %RANDOM
Rwork0.20421 ---
all0.20751 205772 --
obs0.20751 195488 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.626 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å21.16 Å20.58 Å2
2---2.13 Å20.57 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26574 0 962 847 28383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02228098
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.231.98638174
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.80453389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.01125.3041235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.948154691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8341597
X-RAY DIFFRACTIONr_chiral_restr0.1530.24264
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02120772
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_it1.1331.516865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.051227316
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.287311233
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0634.510853
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 706 -
Rwork0.249 13452 -
obs--84.57 %

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