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- PDB-7n63: X-ray structure of HCAN_0200, an aminotransferase from Helicobact... -

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Basic information

Entry
Database: PDB / ID: 7n63
TitleX-ray structure of HCAN_0200, an aminotransferase from Helicobacter canadensis in complex with its external aldimine
ComponentsPutative aminotransferase
KeywordsTRANSFERASE / aminotransferase / pyridoxyl phosphate / external aldimine
Function / homologyDegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / transaminase activity / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Chem-TQP / Putative aminotransferase
Function and homology information
Biological speciesHelicobacter canadensis MIT 98-5491 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGriffiths, W.A. / Heisdorf, 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 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: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,64810
Polymers42,4401
Non-polymers1,2099
Water9,206511
1
A: Putative aminotransferase
hetero molecules

A: Putative aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,29720
Polymers84,8802
Non-polymers2,41718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7540 Å2
ΔGint-1 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.005, 150.766, 91.058
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

MG

21A-547-

HOH

31A-631-

HOH

41A-844-

HOH

51A-963-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative aminotransferase


Mass: 42439.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter canadensis MIT 98-5491 (bacteria)
Gene: HCAN_0204 / Production host: Escherichia coli (E. coli) / References: UniProt: C5ZW06

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Non-polymers , 5 types, 520 molecules

#2: Chemical ChemComp-TQP / (2R,3R,4S,5S,6R)-3,5-dihydroxy-4-{[(1E)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene]amino}-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 776.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H35N4O19P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Enzyme incubated with 1 mM PLP and 5 mM dTDP-3-amino-3,6-dideoxyglucose. Precipitant = 15-18 % PEG 3350, 100 mM MgCl2, 100 mM MES, pH 6.

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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: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 81651 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.068 / Net I/σ(I): 12.7
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 14740 / Rsym value: 0.41 / % possible all: 96.3

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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: 5u1z

5u1z


Resolution: 1.4→35.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.274 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1897 4146 5.1 %RANDOM
Rwork0.1711 ---
obs0.172 77505 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.81 Å2 / Biso mean: 11.104 Å2 / Biso min: 4.53 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.4→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 85 512 3516
Biso mean--17.15 24.08 -
Num. residues----362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172991
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.6434295
X-RAY DIFFRACTIONr_angle_other_deg1.5421.5756985
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4455386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64224.516155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24715581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4471510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02604
LS refinement shellResolution: 1.4→1.436 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 282 -
Rwork0.391 5460 -
all-5742 -
obs--95.08 %

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