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- PDB-4xd1: X-ray structure of the N-formyltransferase QdtF from Providencia ... -

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Basic information

Entry
Database: PDB / ID: 4xd1
TitleX-ray structure of the N-formyltransferase QdtF from Providencia alcalifaciens, W305A mutant, in the presence of TDP-Qui3N and N5-THF
ComponentsTDP-3-aminoquinovose-N-formyltransferase
KeywordsTRANSFERASE / formyltransferase / ankyrin repeat / lipopolysaccharide / deoxy sugar
Function / homology
Function and homology information


hydroxymethyl-, formyl- and related transferase activity / biosynthetic process
Similarity search - Function
Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-FON / : / Chem-T3Q / Qdtf
Similarity search - Component
Biological speciesProvidencia alcalifaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsThoden, J.B. / Woodford, C.R. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2015
Title: New Role for the Ankyrin Repeat Revealed by a Study of the N-Formyltransferase from Providencia alcalifaciens.
Authors: Woodford, C.R. / Thoden, J.B. / Holden, H.M.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_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 / _pdbx_struct_oper_list.symmetry_operation / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TDP-3-aminoquinovose-N-formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,61716
Polymers48,0491
Non-polymers1,56915
Water10,899605
1
A: TDP-3-aminoquinovose-N-formyltransferase
hetero molecules

A: TDP-3-aminoquinovose-N-formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,23432
Polymers96,0972
Non-polymers3,13730
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)78.279, 78.279, 151.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-553-

HOH

21A-593-

HOH

31A-657-

HOH

41A-701-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein TDP-3-aminoquinovose-N-formyltransferase


Mass: 48048.617 Da / Num. of mol.: 1 / Mutation: W305A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Providencia alcalifaciens (bacteria) / Gene: qdtf / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: F8RC03, methionyl-tRNA formyltransferase

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Non-polymers , 7 types, 620 molecules

#2: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H23N7O7
#3: Chemical ChemComp-T3Q / [(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate / thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose


Mass: 547.345 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H27N3O14P2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5-7% PEG 8000, 100 mM HEPPS, 200 mM NaCl, 200 mM KCl, 5 mM TDP, 5 mM N5-THF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Aug 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 73582 / Num. obs: 73582 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 11.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XCZ

4xcz


Resolution: 1.5→35.03 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.606 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20828 3695 5 %RANDOM
Rwork0.17981 ---
obs0.18124 69887 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.55 Å20 Å2
3----1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.5→35.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 97 605 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193437
X-RAY DIFFRACTIONr_bond_other_d00.023282
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9834659
X-RAY DIFFRACTIONr_angle_other_deg0.93237580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0825.438160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94215619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.143157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02785
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: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 247 -
Rwork0.346 4754 -
obs--90.52 %

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