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- PDB-6cgq: Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and ... -

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Basic information

Entry
Database: PDB / ID: 6cgq
TitleThreonine synthase from Bacillus subtilis ATCC 6633 with PLP and PLP-Ala
ComponentsThreonine synthase
KeywordsLYASE / ThrC / threonine synthase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


threonine synthase / threonine synthase activity / threonine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Threonine synthase, bacterial/archaeal / Threonine synthase-like / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-F0G / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Threonine synthase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 Å
AuthorsPetronikolou, N. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)4P01GM077596-10 United States
CitationJournal: ACS Chem. Biol. / Year: 2019
Title: Molecular Basis of Bacillus subtilis ATCC 6633 Self-Resistance to the Phosphono-oligopeptide Antibiotic Rhizocticin.
Authors: Petronikolou, N. / Ortega, M.A. / Borisova, S.A. / Nair, S.K. / Metcalf, W.W.
History
DepositionFeb 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine synthase
B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1105
Polymers75,4502
Non-polymers6603
Water6,648369
1
A: Threonine synthase
hetero molecules

B: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1105
Polymers75,4502
Non-polymers6603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area6490 Å2
ΔGint-57 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.787, 127.933, 237.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-637-

HOH

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Components

#1: Protein Threonine synthase /


Mass: 37724.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. spizizenii (bacteria)
Gene: thrC / Production host: Escherichia coli (E. coli) / References: UniProt: A8HUA2, threonine synthase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-F0G / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-alanine / PLP-Ala


Type: L-peptide linking / Mass: 318.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium L-glutamate, 0.2 M DL-alanine, 0.2 M glycine, 0.2 M DL-lysine HCl, 0.2 M DL-serine, 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.1 M MES/imidazole, pH 6.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.019→118.5 Å / Num. obs: 50330 / % possible obs: 100 % / Redundancy: 8.2 % / Rsym value: 0.127 / Net I/σ(I): 14.6
Reflection shellResolution: 2.019→2.026 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 490 / CC1/2: 0.788 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
autoPROCdata scaling
PHASERphasing
autoPROCdata processing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZSJ

2zsj


Resolution: 2.019→49.719 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2441 4.86 %
Rwork0.1805 --
obs0.183 50265 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.019→49.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5116 0 41 369 5526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075251
X-RAY DIFFRACTIONf_angle_d0.8737128
X-RAY DIFFRACTIONf_dihedral_angle_d3.7093808
X-RAY DIFFRACTIONf_chiral_restr0.051820
X-RAY DIFFRACTIONf_plane_restr0.006931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0194-2.06060.30141540.25652764X-RAY DIFFRACTION100
2.0606-2.10540.30691320.24672765X-RAY DIFFRACTION100
2.1054-2.15440.27181710.23042763X-RAY DIFFRACTION100
2.1544-2.20830.27061580.22382748X-RAY DIFFRACTION100
2.2083-2.2680.2711480.21422778X-RAY DIFFRACTION100
2.268-2.33470.27131450.21362769X-RAY DIFFRACTION100
2.3347-2.41010.27321280.21032795X-RAY DIFFRACTION100
2.4101-2.49620.27841480.19852814X-RAY DIFFRACTION100
2.4962-2.59620.24671530.19692769X-RAY DIFFRACTION100
2.5962-2.71430.24081200.18972803X-RAY DIFFRACTION100
2.7143-2.85740.21271300.18072831X-RAY DIFFRACTION100
2.8574-3.03640.25141520.18482788X-RAY DIFFRACTION100
3.0364-3.27080.24351320.18612864X-RAY DIFFRACTION100
3.2708-3.59990.23771520.17332827X-RAY DIFFRACTION100
3.5999-4.12060.19971350.14752852X-RAY DIFFRACTION100
4.1206-5.19060.17851440.14212870X-RAY DIFFRACTION100
5.1906-49.73450.2011390.16083024X-RAY DIFFRACTION100

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