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- PDB-9d2t: Crystal structure of S. aureus Threonine deaminase regulatory domain -

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Basic information

Entry
Database: PDB / ID: 9d2t
TitleCrystal structure of S. aureus Threonine deaminase regulatory domain
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsLYASE / Staphylococcus aureus / threonine dehydratase / IlvA / isoleucine / branched-chain amino acids / regulation
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / L-serine ammonia-lyase activity / L-threonine catabolic process / L-serine catabolic process / isoleucine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
L-threonine dehydratase biosynthetic IlvA / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme ...L-threonine dehydratase biosynthetic IlvA / Threonine dehydratase, ACT-like domain / Threonine dehydratase, ACT-like domain superfamily / C-terminal regulatory domain of Threonine dehydratase / ACT-like domain profile. / : / Serine/threonine dehydratase, pyridoxal-phosphate-binding site / Serine/threonine dehydratases pyridoxal-phosphate attachment site. / ACT-like domain / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme
Similarity search - Domain/homology
L-threonine dehydratase biosynthetic IlvA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRock, C.O. / Yun, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
CitationJournal: Biochemistry / Year: 2025
Title: Isoleucine Binding and Regulation of Escherichia coli and Staphylococcus aureus Threonine Dehydratase (IlvA).
Authors: Yun, M.K. / Subramanian, C. / Miller, K. / Jackson, P. / Radka, C.D. / Rock, C.O.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._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_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 9, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA
C: L-threonine dehydratase biosynthetic IlvA
D: L-threonine dehydratase biosynthetic IlvA
E: L-threonine dehydratase biosynthetic IlvA
F: L-threonine dehydratase biosynthetic IlvA
H: L-threonine dehydratase biosynthetic IlvA
G: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)99,2498
Polymers99,2498
Non-polymers00
Water25214
1
A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA
C: L-threonine dehydratase biosynthetic IlvA
D: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)49,6244
Polymers49,6244
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area17610 Å2
MethodPISA
2
E: L-threonine dehydratase biosynthetic IlvA
F: L-threonine dehydratase biosynthetic IlvA
H: L-threonine dehydratase biosynthetic IlvA
G: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)49,6244
Polymers49,6244
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-28 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.921, 88.921, 213.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
L-threonine dehydratase biosynthetic IlvA / Threonine deaminase


Mass: 12406.063 Da / Num. of mol.: 8 / Fragment: Regulatory domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: ilvA, SAUSA300_2014 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FF63, threonine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: CAPSO, ammonium sulfate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→44.5 Å / Num. obs: 20172 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 19
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1410 / CC1/2: 0.79 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→44.46 Å / Cross valid method: THROUGHOUT / σ(F): 322.28 / Phase error: 35.9495 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.239 1002 4.98 %
Rwork0.192 19116 -
obs0.1938 20118 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5415 0 0 14 5429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215527
X-RAY DIFFRACTIONf_angle_d0.4277471
X-RAY DIFFRACTIONf_chiral_restr0.0425826
X-RAY DIFFRACTIONf_plane_restr0.003974
X-RAY DIFFRACTIONf_dihedral_angle_d10.03873329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.960.36281490.30242706X-RAY DIFFRACTION94.15
2.96-3.140.32751420.27862710X-RAY DIFFRACTION94.95
3.14-3.380.26671440.24872735X-RAY DIFFRACTION94.97
3.38-3.720.24411400.22972713X-RAY DIFFRACTION94.79
3.72-4.260.26291420.19322728X-RAY DIFFRACTION94.76
4.26-5.360.20971390.15742737X-RAY DIFFRACTION94.97
5.36-30.160.21051460.16282746X-RAY DIFFRACTION94.72
Refinement TLS params.Method: refined / Origin x: 21.84608598 Å / Origin y: -3.31062466305 Å / Origin z: 38.5782177711 Å
111213212223313233
T0.684096735898 Å2-0.0145007898475 Å2-0.0869413938562 Å2-0.711307061022 Å20.0369361183718 Å2--0.420983541304 Å2
L0.126689448635 °20.118943813314 °2-0.299970263761 °2-0.80335232752 °2-0.334201760813 °2--0.729072717981 °2
S0.00887590417027 Å °-0.0289012885066 Å °0.0087991047775 Å °0.072194627892 Å °0.0040292290762 Å °-0.031491653837 Å °-0.13364996047 Å °0.265297619652 Å °-0.00182819785763 Å °
Refinement TLS groupSelection details: all

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