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- PDB-8zkv: Crystal structure of mutant catalytic domains of threonine deamin... -

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Basic information

Entry
Database: PDB / ID: 8zkv
TitleCrystal structure of mutant catalytic domains of threonine deaminase in complex with PLP
ComponentsL-threonine dehydratase biosynthetic IlvA
KeywordsSTRUCTURAL PROTEIN / Threonine Deaminase / Pyridoxal phosphate
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / threonine metabolic process / branched-chain amino acid biosynthetic process / isoleucine biosynthetic process / amino acid binding / pyridoxal phosphate binding
Similarity search - Function
Threonine dehydratase, biosynthetic / 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 ...Threonine dehydratase, biosynthetic / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsKhodi, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Dimer-Tetramer Transition Modulates the Allosteric Regulation of Threonine Deaminase
Authors: Khodi, S. / Yekeen, A. / Liu, H. / Chen, Q.
History
DepositionMay 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine / refine_hist / refine_ls_shell / reflns / reflns_shell / struct / struct_asym / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.title / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_obs / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _reflns.d_resolution_low / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_Rpim_I_all / _reflns.pdbx_Rrim_I_all / _reflns.pdbx_netI_over_sigmaI / _reflns.percent_possible_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rrim_I_all / _reflns_shell.percent_possible_all / _struct.title / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 18, 2024Group: Derived calculations / Category: struct_conf

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,54819
Polymers142,1114
Non-polymers1,43715
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9960 Å2
ΔGint-228 kcal/mol
Surface area47390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.567, 83.808, 143.245
Angle α, β, γ (deg.)90.00, 112.51, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 35527.723 Da / Num. of mol.: 4 / Mutation: H322L,S328L,G334L
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 1.5 M (NH4)2SO4 and 0.1 M Tris pH 8.5

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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: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.56→40.38 Å / Num. obs: 52178 / % possible obs: 99.83 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1379 / Rpim(I) all: 0.05753 / Rrim(I) all: 0.1496 / Χ2: 1 / Net I/σ(I): 9.9
Reflection shellResolution: 2.56→2.64 Å / Rmerge(I) obs: 0.9016 / Num. unique obs: 5170 / CC1/2: 0.756 / Rpim(I) all: 0.3744 / Rrim(I) all: 0.9775 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDJ

1tdj


Resolution: 2.56→40.38 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 2495 4.78 %
Rwork0.1829 --
obs0.1853 52142 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→40.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9868 0 70 98 10036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610100
X-RAY DIFFRACTIONf_angle_d0.71313704
X-RAY DIFFRACTIONf_dihedral_angle_d6.8241431
X-RAY DIFFRACTIONf_chiral_restr0.0481577
X-RAY DIFFRACTIONf_plane_restr0.0051777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.31791230.25195170X-RAY DIFFRACTION98
2.61-2.660.30991440.23922747X-RAY DIFFRACTION100
2.66-2.720.32661180.23742751X-RAY DIFFRACTION100
2.72-2.780.36891270.23132782X-RAY DIFFRACTION100
2.78-2.850.25781440.21242741X-RAY DIFFRACTION100
2.85-2.930.26171510.22222749X-RAY DIFFRACTION100
2.93-3.020.32111270.21932770X-RAY DIFFRACTION100
3.02-3.110.33931480.22962736X-RAY DIFFRACTION100
3.11-3.220.31061420.232754X-RAY DIFFRACTION100
3.22-3.350.28721530.20912718X-RAY DIFFRACTION100
3.35-3.510.25661280.20062803X-RAY DIFFRACTION100
3.51-3.690.27431420.18922765X-RAY DIFFRACTION100
3.69-3.920.18381420.16362723X-RAY DIFFRACTION100
3.92-4.220.15681280.15362802X-RAY DIFFRACTION100
4.22-4.650.18451220.13492791X-RAY DIFFRACTION100
4.65-5.320.18561580.15112770X-RAY DIFFRACTION100
5.32-6.70.2281400.17962784X-RAY DIFFRACTION100
6.7-8.10.18411580.1562813X-RAY DIFFRACTION99

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