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- PDB-7n7c: crystal structure of the N-formyltransferase HCAN_0200 from helic... -

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Basic information

Entry
Database: PDB / ID: 7n7c
Titlecrystal structure of the N-formyltransferase HCAN_0200 from helicobacter canadensis in complex with folinic acid and dTDP-3-aminoquinovose
ComponentsFormyl_trans_N domain-containing protein
KeywordsTRANSFERASE / folinic acid / formyltransferase / aminoquinovose
Function / homologymethionyl-tRNA formyltransferase activity / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Chem-FON / : / Chem-T3Q / Formyl transferase N-terminal domain-containing protein
Function and homology information
Biological speciesHelicobacter canadensis MIT 98-5491 (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHeisdorf, C.J. / Thoden, J.B. / Holden, H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM134643 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Investigation of the enzymes required for the biosynthesis of an unusual formylated sugar in the emerging human pathogen Helicobacter canadensis.
Authors: Heisdorf, C.J. / Griffiths, W.A. / Thoden, J.B. / Holden, H.M.
History
DepositionJun 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Sep 22, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formyl_trans_N domain-containing protein
B: Formyl_trans_N domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,43711
Polymers66,1312
Non-polymers2,3069
Water7,945441
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-5 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.997, 74.039, 82.328
Angle α, β, γ (deg.)90.000, 115.040, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Formyl_trans_N domain-containing protein


Mass: 33065.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter canadensis MIT 98-5491 (bacteria)
Gene: HCAN_0200 / Production host: Escherichia coli (E. coli) / References: UniProt: C5ZW02

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Non-polymers , 5 types, 450 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.: 2 / Source method: obtained synthetically / Formula: C20H23N7O7 / Feature type: SUBJECT OF INVESTIGATION
#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.: 2 / Source method: obtained synthetically / Formula: C16H27N3O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 11-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5) Crystals soaked in 26% PEG-8000, 600 mM NaCl, 5 mM folinic acid, 10 mM dTDP-3-aminoquinovose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 46424 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rsym value: 0.073 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 6240 / Rsym value: 0.347 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7n7a

7n7a


Resolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.885 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 2336 5 %RANDOM
Rwork0.1818 ---
obs0.1843 44088 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 26.632 Å2 / Biso min: 11.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4480 0 152 441 5073
Biso mean--33.37 31.09 -
Num. residues----540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134745
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174286
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.6426411
X-RAY DIFFRACTIONr_angle_other_deg1.3051.5749990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2735540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.04624.524252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28215835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025181
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02999
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 170 -
Rwork0.3 3235 -
all-3405 -
obs--97.99 %

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