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- PDB-2gn1: Crystal structure of dimeric biodegradative threonine deaminase (... -

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Basic information

Entry
Database: PDB / ID: 2gn1
TitleCrystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 2.2A resolution (Triclinic form with one dimer of TdcB in the asymmetric unit)
ComponentsThreonine dehydratase catabolic
KeywordsLYASE / TdcB / Biodegradative threonine deaminase / PLP / CMP / Threonine dehydratase / L-threonine metabolism
Function / homology
Function and homology information


threonine ammonia-lyase / threonine deaminase activity / L-threonine catabolic process to propionate / L-serine ammonia-lyase / L-serine ammonia-lyase activity / threonine catabolic process / 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: 2.2 Å
AuthorsSimanshu, D.K. / Savithri, H.S. / Murthy, M.R.N.
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 / 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_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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,7973
Polymers73,7742
Non-polymers231
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-17 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.317, 55.300, 67.235
Angle α, β, γ (deg.)103.09, 94.70, 112.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Threonine dehydratase catabolic / Threonine deaminase


Mass: 36887.086 Da / Num. of mol.: 2
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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 40.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M citrate buffer pH 6.0, 20% PEG 3350 and 10% 2-propanol, 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: Dec 24, 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: 2.2→30 Å / Num. obs: 29556 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Redundancy: 12.19 % / Biso Wilson estimate: 31.42 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 22.18
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 4.98 / Num. unique all: 2494 / % possible all: 84.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BIODEGRADATIVE THREONINE DEAMINASE FROM SALMONELLA TYPHIMURIUM (PDB CODE 1GN0)

1gn0


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.718 / SU ML: 0.185 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.431 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25291 1405 5 %RANDOM
Rwork0.20964 ---
obs0.21183 26557 94.32 %-
all-26557 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.816 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å22.34 Å20.94 Å2
2--2.5 Å20.92 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 1 274 5064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0224857
X-RAY DIFFRACTIONr_bond_other_d0.0010.024564
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9776575
X-RAY DIFFRACTIONr_angle_other_deg0.741310598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.475648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66624.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4821527
X-RAY DIFFRACTIONr_chiral_restr0.0560.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02891
X-RAY DIFFRACTIONr_nbd_refined0.180.21143
X-RAY DIFFRACTIONr_nbd_other0.1570.24955
X-RAY DIFFRACTIONr_nbtor_refined0.1630.22424
X-RAY DIFFRACTIONr_nbtor_other0.0790.22884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2257
X-RAY DIFFRACTIONr_metal_ion_refined0.0430.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.24
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1040.21
X-RAY DIFFRACTIONr_mcbond_it0.3121.53195
X-RAY DIFFRACTIONr_mcbond_other0.0571.51347
X-RAY DIFFRACTIONr_mcangle_it0.56325127
X-RAY DIFFRACTIONr_scbond_it0.88531684
X-RAY DIFFRACTIONr_scangle_it1.5384.51447
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 79 -
Rwork0.229 1637 -
obs-1637 79.08 %
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)
11.23190.2534-0.90492.7504-1.13163.1334-0.06170.0611-0.0893-0.17260.15480.02520.2789-0.0934-0.0931-0.1815-0.0086-0.0295-0.1626-0.0234-0.18770.4177-0.20970.4593
21.5448-0.7612-0.17331.6241-0.21662.68570.08390.02120.2004-0.04050.07930.0143-0.2448-0.2145-0.1632-0.09310.01930.0225-0.0570.0215-0.0855-13.22635.85432.7834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 32512 - 338
2X-RAY DIFFRACTION2BB5 - 32518 - 338

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