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- PDB-7n7a: crystal structure of the dTDP-Qui3N N-formyltransferase from Heli... -

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Basic information

Entry
Database: PDB / ID: 7n7a
Titlecrystal structure of the dTDP-Qui3N N-formyltransferase from Helicobacter canadensis, apo form
ComponentsFormyl_trans_N domain-containing protein
KeywordsTRANSFERASE / folate / formyltransferase
Function / homologymethionyl-tRNA formyltransferase activity / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / cytosol / Formyl transferase N-terminal domain-containing protein
Function and homology information
Biological speciesHelicobacter canadensis MIT 98-5491 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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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)66,5669
Polymers66,1312
Non-polymers4347
Water12,412689
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint5 kcal/mol
Surface area25150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.956, 74.701, 82.284
Angle α, β, γ (deg.)90.000, 113.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 11-14% PEG-8000, 2% DMSO, 100 mM homopipes (pH 5)

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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 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 65901 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.059 / Net I/σ(I): 18.7
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.9 / Num. unique obs: 7018 / Rsym value: 0.267 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.27data extraction
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lxq

4lxq


Resolution: 1.8→29.67 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.674 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3232 4.9 %RANDOM
Rwork0.1673 ---
obs0.169 62669 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.51 Å2 / Biso mean: 20.084 Å2 / Biso min: 6.45 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4475 0 28 695 5198
Biso mean--33.43 30.14 -
Num. residues----539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174261
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.6386253
X-RAY DIFFRACTIONr_angle_other_deg1.4061.5739932
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9165549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83124.567254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68115846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4011511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025111
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02986
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 236 -
Rwork0.342 4552 -
all-4788 -
obs--97.38 %

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