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- PDB-4nv1: Crystal structure of a 4-N formyltransferase from Francisella tul... -

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Basic information

Entry
Database: PDB / ID: 4nv1
TitleCrystal structure of a 4-N formyltransferase from Francisella tularensis
ComponentsFormyltransferase
KeywordsTRANSFERASE / FMT formyltransferase / N-10-formyl-tetrahydrofolate / formylation
Function / homology
Function and homology information


methionyl-tRNA formyltransferase activity / cytosol
Similarity search - Function
N-formyltransferase dimerization C-terminal domain / N-formyltransferase dimerization C-terminal domain / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
dTDP-4-amino-4,6-dideoxyglucose / dTDP-4,6-dideoxy-4-formamido-glucose / PHOSPHATE ION / THYMIDINE-5'-DIPHOSPHATE / Formyl transferase / Formyltransferase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsThoden, J.B. / Zimmer, A.L. / Holden, H.M.
CitationJournal: Protein Sci. / Year: 2014
Title: Three-dimensional structure of a sugar N-formyltransferase from Francisella tularensis.
Authors: Zimmer, A.L. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: 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 / 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 / _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
C: Formyltransferase
D: Formyltransferase
E: Formyltransferase
F: Formyltransferase
B: Formyltransferase
A: Formyltransferase
G: Formyltransferase
H: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,95121
Polymers224,5048
Non-polymers4,44613
Water13,187732
1
C: Formyltransferase
D: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1715
Polymers56,1262
Non-polymers1,0453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-36 kcal/mol
Surface area23750 Å2
MethodPISA
2
E: Formyltransferase
F: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1715
Polymers56,1262
Non-polymers1,0453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-36 kcal/mol
Surface area23660 Å2
MethodPISA
3
B: Formyltransferase
A: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3445
Polymers56,1262
Non-polymers1,2183
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-31 kcal/mol
Surface area23410 Å2
MethodPISA
4
G: Formyltransferase
H: Formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2666
Polymers56,1262
Non-polymers1,1394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-44 kcal/mol
Surface area23780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.942, 80.065, 109.852
Angle α, β, γ (deg.)71.72, 88.62, 89.78
Int Tables number1
Space group name H-MP1
DetailsThe symmetric unit deposited contains FOUR dimers

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Components

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Protein , 1 types, 8 molecules CDEFBAGH

#1: Protein
Formyltransferase


Mass: 28063.061 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: Schu S4 / Gene: wbtJ / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q79RC8, UniProt: Q5NF01*PLUS

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Non-polymers , 5 types, 745 molecules

#2: Chemical
ChemComp-0FX / dTDP-4-amino-4,6-dideoxyglucose


Mass: 547.345 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE


Mass: 402.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N2O11P2
#5: Chemical ChemComp-4TG / dTDP-4,6-dideoxy-4-formamido-glucose


Mass: 575.355 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12-15% PEG8000, 100 mM HEPPS, 5 mM dTDP-Qui4NFo, 5 mM N5-THF, 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
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 121975 / Num. obs: 121975 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 3.9 / Num. unique all: 11250 / Rsym value: 0.231 / % possible all: 82.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
SOLVEphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→29.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.161 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.247 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: S
RfactorNum. reflection% reflectionSelection details
Rfree0.27038 6149 5 %RANDOM
Rwork0.19145 ---
all0.195 121975 --
obs0.19536 115826 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.769 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0.82 Å20.63 Å2
2---0.51 Å2-0.81 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15672 0 277 732 16681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01916311
X-RAY DIFFRACTIONr_bond_other_d0.0010.0215486
X-RAY DIFFRACTIONr_angle_refined_deg2.2931.9722065
X-RAY DIFFRACTIONr_angle_other_deg0.957335814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47851923
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31325.635795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.041152978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3371540
X-RAY DIFFRACTIONr_chiral_restr0.1210.22424
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218117
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023662
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.102→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 390 -
Rwork0.266 7808 -
obs--81.51 %

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