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- PDB-7n67: Crystal structure of HCAN_0198, a 3,4-ketoisomerase from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 7n67
TitleCrystal structure of HCAN_0198, a 3,4-ketoisomerase from Helicobacter canadensis
ComponentsFdtA domain-containing protein
KeywordsISOMERASE / ketoisomerase / helicobacter
Function / homologySugar 3,4-ketoisomerase QdtA, cupin domain / WxcM-like, C-terminal / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / TETRAMETHYLAMMONIUM ION / THYMIDINE-5'-DIPHOSPHATE / FdtA domain-containing protein
Function and homology information
Biological speciesHelicobacter canadensis MIT 98-5491 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHeisdorf, C.J. / Griffiths, W.A. / 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 7, 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 / _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: FdtA domain-containing protein
B: FdtA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3345
Polymers36,4552
Non-polymers8793
Water2,216123
1
A: FdtA domain-containing protein
B: FdtA domain-containing protein
hetero molecules

A: FdtA domain-containing protein
B: FdtA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,66710
Polymers72,9104
Non-polymers1,7576
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area13260 Å2
ΔGint-75 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.944, 92.944, 85.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

#1: Protein FdtA domain-containing protein


Mass: 18227.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter canadensis MIT 98-5491 (bacteria)
Gene: HCAN_0198 / Production host: Escherichia coli (E. coli) / References: UniProt: C5ZW00
#2: Chemical ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE / Thymidine diphosphate


Mass: 402.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TMA / TETRAMETHYLAMMONIUM ION / Tetramethylammonium


Mass: 74.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein incubated with 5 mM TDP. precipitant = 7-13% PEG-8000, 1 M tetramethyl ammonium chloride, 100 mM HEPES (pH 7.5)

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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: Mar 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14924 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.1 % / Rsym value: 0.048 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1656 / Rsym value: 0.346 / % possible all: 98.7

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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: 5tpu

5tpu


Resolution: 2.5→24.79 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.076 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 733 4.9 %RANDOM
Rwork0.2004 ---
obs0.2044 14191 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.79 Å2 / Biso mean: 35.853 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.04 Å20 Å2
2---0.09 Å20 Å2
3---0.29 Å2
Refinement stepCycle: final / Resolution: 2.5→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 55 123 2383
Biso mean--39.56 33.16 -
Num. residues----265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172125
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.6433127
X-RAY DIFFRACTIONr_angle_other_deg1.1891.5844926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5665265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60222.361144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0261518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02511
LS refinement shellResolution: 2.5→2.564 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 61 -
Rwork0.267 1010 -
all-1071 -
obs--98.98 %

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