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- PDB-4k2m: Crystal structure of ntda from bacillus subtilis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4k2m
TitleCrystal structure of ntda from bacillus subtilis in complex with the plp external aldimine adduct with kanosamine-6-phosphate
ComponentsNTD biosynthesis operon protein NtdA
KeywordsTRANSFERASE / Sugar aminotransferase / Aspertate aminotransferase fold / homo-dimer / additional N-terninal domain / 3-KETO-GLUCOSE-6-PHOSPHATE AMINITRANSFERASE / KANOSAMINE-6-PHOSPHATE
Function / homology
Function and homology information


3-dehydro-glucose-6-phosphate-glutamate transaminase / polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-O1G / 3-oxo-glucose-6-phosphate:glutamate aminotransferase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.71 Å
AuthorsVan Straaten, K.E. / Palmer, D.R.J. / Sanders, D.A.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Structure of NtdA, a Sugar Aminotransferase Involved in the Kanosamine Biosynthetic Pathway in Bacillus subtilis, Reveals a New Subclass of Aminotransferases.
Authors: van Straaten, K.E. / Ko, J.B. / Jagdhane, R. / Anjum, S. / Palmer, D.R. / Sanders, D.A.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NTD biosynthesis operon protein NtdA
B: NTD biosynthesis operon protein NtdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,25314
Polymers100,6652
Non-polymers1,58812
Water16,844935
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-1 kcal/mol
Surface area33630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.700, 106.440, 98.240
Angle α, β, γ (deg.)90.00, 96.42, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a homo-dimer

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Components

#1: Protein NTD biosynthesis operon protein NtdA


Mass: 50332.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: 939788, BSU10550, NP_388936.1, ntdA, yhjL / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold (DE3) / References: UniProt: O07566
#2: Sugar ChemComp-O1G / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco pyranose / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-alpha-D-gluco se / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-D-glucose / 3-deoxy-3-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 488.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H22N2O13P2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 295 K / pH: 5.6
Details: 0.1M tri-sodium citrate pH 5.6, 0.2M ammonium acetate, 10-30% PEG3350, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 6, 2011 / Details: MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.71→46.8 Å / Num. obs: 108740 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.28
Reflection shellResolution: 1.71→1.75 Å / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.14 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.86 Å46.73 Å
Translation1.86 Å46.73 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4K2B

4k2b


Resolution: 1.71→46.73 Å / Occupancy max: 1 / Occupancy min: 0.34 / SU ML: 0.16 / Isotropic thermal model: Isotropic / σ(F): 1.99 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 5437 5 %
Rwork0.152 --
obs0.154 108734 99.3 %
all-432120 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.24 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.6499 Å20 Å23.9037 Å2
2---5.9402 Å20 Å2
3---2.2903 Å2
Refinement stepCycle: LAST / Resolution: 1.71→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7055 0 102 935 8092
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077420
X-RAY DIFFRACTIONf_angle_d1.1310041
X-RAY DIFFRACTIONf_dihedral_angle_d13.9022809
X-RAY DIFFRACTIONf_chiral_restr0.0791122
X-RAY DIFFRACTIONf_plane_restr0.0051287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7099-1.72940.27261780.23913397X-RAY DIFFRACTION98
1.7294-1.74970.23891790.22333394X-RAY DIFFRACTION98
1.7497-1.77110.25521800.21413418X-RAY DIFFRACTION99
1.7711-1.79350.26281780.20933382X-RAY DIFFRACTION99
1.7935-1.81710.25951800.1993417X-RAY DIFFRACTION99
1.8171-1.8420.21781820.19163465X-RAY DIFFRACTION99
1.842-1.86830.21391790.17143393X-RAY DIFFRACTION99
1.8683-1.89620.19851800.17043421X-RAY DIFFRACTION99
1.8962-1.92580.21641810.16423444X-RAY DIFFRACTION99
1.9258-1.95740.2121780.17013388X-RAY DIFFRACTION99
1.9574-1.99110.18921830.15253475X-RAY DIFFRACTION99
1.9911-2.02730.17861780.15023375X-RAY DIFFRACTION99
2.0273-2.06630.18941830.15163477X-RAY DIFFRACTION99
2.0663-2.10850.19241790.14873406X-RAY DIFFRACTION99
2.1085-2.15440.19371820.14773453X-RAY DIFFRACTION99
2.1544-2.20450.18361800.14553425X-RAY DIFFRACTION100
2.2045-2.25960.18411850.14673514X-RAY DIFFRACTION100
2.2596-2.32070.18231780.14493386X-RAY DIFFRACTION100
2.3207-2.3890.18161820.14763459X-RAY DIFFRACTION100
2.389-2.46610.20521830.14973462X-RAY DIFFRACTION100
2.4661-2.55420.17251810.14643445X-RAY DIFFRACTION100
2.5542-2.65650.17561820.14693463X-RAY DIFFRACTION100
2.6565-2.77740.1811830.13963474X-RAY DIFFRACTION100
2.7774-2.92380.16931830.14763475X-RAY DIFFRACTION100
2.9238-3.10690.17051820.14673461X-RAY DIFFRACTION100
3.1069-3.34680.18681820.14543457X-RAY DIFFRACTION100
3.3468-3.68340.16571820.1433457X-RAY DIFFRACTION100
3.6834-4.21610.1531830.12673487X-RAY DIFFRACTION100
4.2161-5.31070.16661840.13583485X-RAY DIFFRACTION100
5.3107-46.7450.20651870.173542X-RAY DIFFRACTION99

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