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- PDB-2gn0: Crystal structure of dimeric biodegradative threonine deaminase (... -

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Basic information

Entry
Database: PDB / ID: 2gn0
TitleCrystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)
ComponentsThreonine dehydratase catabolic
KeywordsLYASE / TdcB / Biodegradative threonine deaminase / PLP / Threonine dehydratase / L-threonine metabolism / Alternate conformation
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / L-threonine catabolic process to propionate / threonine catabolic process / L-serine ammonia-lyase / L-serine ammonia-lyase activity / L-serine catabolic process / isoleucine biosynthetic process / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Threonine dehydratase, catabolic / 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
L-threonine dehydratase catabolic TdcB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSimanshu, D.K. / Savithri, H.S. / Murthy, M.R.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Crystal structures of Salmonella typhimurium biodegradative threonine deaminase and its complex with CMP provide structural insights into ligand-induced oligomerization and enzyme activation.
Authors: Simanshu, D.K. / Savithri, H.S. / Murthy, M.R.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray crystallographic analysis of biodegradative threonine deaminase (TdcB) from Salmonella typhimurium
Authors: Simanshu, D.K. / Chittori, S. / Savithri, H.S. / Murthy, M.R.
History
DepositionApr 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine dehydratase catabolic
B: Threonine dehydratase catabolic
C: Threonine dehydratase catabolic
D: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,5946
Polymers147,5484
Non-polymers462
Water14,052780
1
A: Threonine dehydratase catabolic
B: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7973
Polymers73,7742
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-17 kcal/mol
Surface area23300 Å2
MethodPISA
2
C: Threonine dehydratase catabolic
D: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7973
Polymers73,7742
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-16 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.675, 76.827, 78.501
Angle α, β, γ (deg.)66.12, 89.16, 77.08
Int Tables number1
Space group name H-MP1
Number of models2
DetailsThe biological assembly is a dimer. In this crystal form, asymmetric unit contains four subunits A, B, C and D. AB and CD form two independent biological assembly.

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Components

#1: Protein
Threonine dehydratase catabolic / Threonine deaminase


Mass: 36887.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: IFO 12529 / Gene: tdcB / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P11954, threonine ammonia-lyase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.06 Å3/Da / Density % sol: 40.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M citrate buffer pH 6.0, 20% PEG 3350 and 15% t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 30, 2005 / Details: Osmic mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 128680 / Num. obs: 128680 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 15.64 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.58
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.76 / Num. unique all: 11167 / % possible all: 86.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Biosynthetic threonine deaminase (1TDJ)

1tdj


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.769 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22154 5998 5 %RANDOM
Rwork0.18842 ---
obs0.1901 113742 92.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.819 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.33 Å20.31 Å2
2---0.64 Å20.01 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9636 0 2 780 10418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02212264
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211542
X-RAY DIFFRACTIONr_angle_refined_deg1.0311.97916618
X-RAY DIFFRACTIONr_angle_other_deg0.712326850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10651638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.14824.696460
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49152145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5261570
X-RAY DIFFRACTIONr_chiral_restr0.0570.21974
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022254
X-RAY DIFFRACTIONr_nbd_refined0.1950.22247
X-RAY DIFFRACTIONr_nbd_other0.160.210150
X-RAY DIFFRACTIONr_nbtor_refined0.1660.25485
X-RAY DIFFRACTIONr_nbtor_other0.0790.25702
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2612
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.2124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.225
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0340.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1030.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3671.58008
X-RAY DIFFRACTIONr_mcbond_other0.0921.53373
X-RAY DIFFRACTIONr_mcangle_it0.666212882
X-RAY DIFFRACTIONr_scbond_it1.18734313
X-RAY DIFFRACTIONr_scangle_it1.9794.53723
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 389 -
Rwork0.315 7473 -
obs-7473 83.46 %
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)
11.5021-0.2372-0.36561.970.15910.95980.04060.0051-0.09910.0425-0.07370.08110.0433-0.09350.0331-0.1226-0.0126-0.0256-0.10590.0011-0.143156.2783-0.6124-0.0704
21.1388-0.0743-0.3452.00760.21941.3470.04140.00010.0425-0.1135-0.0495-0.1837-0.06470.0570.0081-0.08650.0120.0015-0.10.0223-0.128355.955734.60763.8479
31.6788-0.4617-0.49541.94980.28121.19890.02840.0443-0.10920.092-0.04940.13540.0217-0.11860.0209-0.1236-0.0085-0.018-0.10830.0035-0.12637.243152.838635.8201
41.08530.1912-0.45841.2175-0.03941.06540.0201-0.0574-0.00120.0296-0.0043-0.0152-0.01980.0403-0.0158-0.1039-0.0134-0.0257-0.08630.024-0.124538.161489.119339.7866
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 325
2X-RAY DIFFRACTION2B6 - 325
3X-RAY DIFFRACTION3C-2 - 325
4X-RAY DIFFRACTION4D6 - 325

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