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- PDB-6nmx: Threonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA -

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Basic information

Entry
Database: PDB / ID: 6nmx
TitleThreonine synthase from Bacillus subtilis ATCC 6633 with PLP and APPA
ComponentsThreonine synthase
KeywordsLYASE / ThrC / threonine synthase
Function / homology
Function and homology information


threonine synthase / threonine deaminase activity / threonine synthase activity / L-serine ammonia-lyase activity / threonine catabolic process / L-serine catabolic process / threonine biosynthetic process / isoleucine 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold ...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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LJS / Threonine synthase
Similarity search - Component
Biological speciesBacillus subtilis subsp. spizizenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.971 Å
AuthorsPetronikolou, N. / Nair, S.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM077596 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127659 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
DepositionJan 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 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 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / refine / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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
C: Threonine synthase
D: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,5978
Polymers150,9004
Non-polymers1,6974
Water15,223845
1
A: Threonine synthase
C: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2984
Polymers75,4502
Non-polymers8482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-46 kcal/mol
Surface area23010 Å2
MethodPISA
2
B: Threonine synthase
D: Threonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2984
Polymers75,4502
Non-polymers8482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-49 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.532, 104.174, 125.573
Angle α, β, γ (deg.)90.00, 99.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Threonine synthase


Mass: 37724.918 Da / Num. of mol.: 4
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-LJS / (2E,3Z)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-5-phosphonopent-3-enoic acid


Mass: 424.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H18N2O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 845 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 282.15 K / Method: vapor diffusion, hanging drop
Details: 0.03 M MgCl2 hexahydrate, 0.03 M CaCl2 dihydrate, 18% v/v PEG 550 MME, 9% w/v PEG 20,000, 0.1 M MES/imidazole, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.971→123.828 Å / Num. obs: 80962 / % possible obs: 91.3 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.067 / Rrim(I) all: 0.145 / Net I/σ(I): 10.7 / Num. measured all: 379109
Reflection shellResolution: 1.971→1.978 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.744 / Num. unique obs: 903 / CC1/2: 0.732 / Rpim(I) all: 0.437 / Rrim(I) all: 0.959 / % possible all: 95.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.64 Å123.83 Å
Translation6.64 Å123.83 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
autoPROCdata scaling
PHASER2.7.12phasing
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CGQ

6cgq


Resolution: 1.971→123.828 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 3846 4.94 %
Rwork0.1586 --
obs0.1613 80926 91.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.971→123.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10431 0 108 845 11384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710719
X-RAY DIFFRACTIONf_angle_d0.91914546
X-RAY DIFFRACTIONf_dihedral_angle_d4.1276506
X-RAY DIFFRACTIONf_chiral_restr0.0511659
X-RAY DIFFRACTIONf_plane_restr0.0051900
LS refinement shellResolution: 1.971→1.9943 Å
RfactorNum. reflection
Rfree0.2973 141
Rwork0.2307 -
obs-2859

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