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- PDB-8zlv: Asymmetric Dimeric Structure of the Catalytic Domain in Truncated... -

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Basic information

Entry
Database: PDB / ID: 8zlv
TitleAsymmetric Dimeric Structure of the Catalytic Domain in Truncated Threonine Deaminase
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsSTRUCTURAL PROTEIN / Threonine Deaminase / PLP
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / L-serine ammonia-lyase activity / threonine catabolic process / branched-chain amino acid biosynthetic process / L-serine catabolic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Threonine dehydratase, ACT-like domain / Threonine dehydratase, biosynthetic / 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 ...Threonine dehydratase, ACT-like domain / Threonine dehydratase, biosynthetic / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKhodi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Engineering Threonine Deaminase Catalytic Domain into a Tetrameric Configuration, Independent of Allosteric Regulation
Authors: Khodi, S.
History
DepositionMay 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-threonine dehydratase biosynthetic IlvA
B: L-threonine dehydratase biosynthetic IlvA


Theoretical massNumber of molelcules
Total (without water)70,2932
Polymers70,2932
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.159, 102.159, 116.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 35146.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ilvA, b3772, JW3745 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04968, threonine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M CaCl2H4O2, 0.1 M HEPES sodium pH 7.5 and 28% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→46.78 Å / Num. obs: 14200 / % possible obs: 99.8 % / Redundancy: 20.3 % / Biso Wilson estimate: 69.55 Å2 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.051 / Rrim(I) all: 0.232 / Χ2: 1.1 / Net I/σ(I): 13.1
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 21.2 % / Rmerge(I) obs: 1.744 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1409 / Rpim(I) all: 0.386 / Rrim(I) all: 1.787 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PHENIX1.19.2-4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDJ

1tdj


Resolution: 2.9→45.69 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 740 5.21 %
Rwork0.2137 --
obs0.2165 14200 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 0 46 4876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034964
X-RAY DIFFRACTIONf_angle_d0.6516725
X-RAY DIFFRACTIONf_dihedral_angle_d6.999711
X-RAY DIFFRACTIONf_chiral_restr0.045771
X-RAY DIFFRACTIONf_plane_restr0.005879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.120.33721390.27562638X-RAY DIFFRACTION100
3.12-3.440.30021450.252658X-RAY DIFFRACTION100
3.44-3.940.30131640.23822624X-RAY DIFFRACTION99
3.94-4.960.26411430.18552686X-RAY DIFFRACTION100
4.96-45.690.2331490.19822854X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2343-1.98580.30833.4311-0.83073.19140.3233-0.2034-0.2707-0.1888-0.02840.3634-0.0113-0.1167-0.16870.32860.00370.03270.3802-0.02880.331320.85575.93350.9844
24.94961.3908-2.22312.17880.02875.4509-0.41060.7736-0.0381-0.57150.15990.2346-0.1788-0.51340.18630.4958-0.0462-0.09490.4608-0.04020.279721.3433.8245-19.3162
32.67280.2941-0.8651.59920.20024.4834-0.14610.3242-0.4125-0.2959-0.0072-0.14960.1131-0.14430.15480.2632-0.02470.04840.2989-0.0120.397228.48244.95-10.1861
41.9196-0.1658-0.60758.00371.68490.41010.01330.63350.2419-0.65590.2708-0.9651-0.1404-0.3462-0.53150.48240.06440.13180.77330.20540.65845.44961.3148-10.2472
54.091.7291-0.49831.60190.53012.1574-0.0193-0.4239-0.5622-0.40760.1106-0.3953-0.20980.02870.07230.4462-0.01510.03490.5010.11390.443238.5784.4543-6.5494
61.809-1.09370.74213.7944-1.98482.5910.17640.1673-0.3652-0.2825-0.1308-0.07880.32550.30360.00090.37040.01750.0510.47660.05190.5428.443-9.49833.9139
73.1732-1.6792-0.13762.8867-0.52144.5790.022-0.1728-0.5207-0.3677-0.01150.18140.2110.1349-0.2080.46170.0115-0.07850.3602-0.00760.5348-1.4518-17.60420.3098
81.170.1182.22655.7031-0.21276.3613-0.1011-0.2222-0.56670.51840.69610.17110.11280.4167-0.41960.59460.19620.07910.7778-0.04570.61373.973-26.443219.6754
93.5191-1.1091-2.31983.1958-0.19952.08-0.06960.1618-0.73260.0231-0.06350.36160.20780.00360.14440.6381-0.042-0.22820.4715-0.11310.7747-3.1761-30.9027-1.977
103.06751.48880.20034.57810.72573.23520.46240.0854-0.4471-0.3346-0.2179-0.14760.28570.3515-0.10130.62640.1338-0.04820.4494-0.08090.432712.1314-24.4169-8.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 114 )
3X-RAY DIFFRACTION3chain 'A' and (resid 115 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 237 )
5X-RAY DIFFRACTION5chain 'A' and (resid 238 through 266 )
6X-RAY DIFFRACTION6chain 'A' and (resid 267 through 336 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 72 )
8X-RAY DIFFRACTION8chain 'B' and (resid 73 through 159 )
9X-RAY DIFFRACTION9chain 'B' and (resid 160 through 266 )
10X-RAY DIFFRACTION10chain 'B' and (resid 267 through 334 )

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