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- PDB-2gn2: Crystal structure of tetrameric biodegradative threonine deaminas... -

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Basic information

Entry
Database: PDB / ID: 2gn2
TitleCrystal structure of tetrameric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium in complex with CMP at 2.5A resolution (Hexagonal form)
ComponentsThreonine dehydratase catabolic
KeywordsLYASE / TdcB / Biodegradative threonine deaminase / PLP / CMP / Threonine dehydratase / L-threonine metabolism
Function / homology
Function and homology information


threonine ammonia-lyase / L-threonine catabolic process to propionate / threonine deaminase activity / L-serine ammonia-lyase / L-serine ammonia-lyase activity / L-serine catabolic 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / L-threonine dehydratase catabolic TdcB
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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

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Assembly

Deposited unit
A: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2333
Polymers36,8871
Non-polymers3462
Water1,11762
1
A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules

A: Threonine dehydratase catabolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,93312
Polymers147,5484
Non-polymers1,3858
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation10_445-y-1,-x-1,-z1
Unit cell
Length a, b, c (Å)161.145, 161.145, 68.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21A-462-

HOH

31A-463-

HOH

DetailsThe monomeric molecule is centered at the point of 222 symmetry. The biological assembly is a teramer generated from the monomer in the asymmetric unit by the operations: -Y,-X,-Z ; -X, -Y, Z; Y, X, -Z.

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Components

#1: Protein Threonine dehydratase catabolic / Threonine deaminase


Mass: 36887.086 Da / Num. of mol.: 1
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: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Citrate, 25% PEG4000, 10% Hexanediol , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.93 Å
DetectorType: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Mar 20, 2006 / Details: Osmic mirror
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 18675 / Num. obs: 18675 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 39.32 % / Biso Wilson estimate: 66 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 53.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 7.56 / Num. unique all: 1820 / % possible all: 100

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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: 2.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 13.455 / SU ML: 0.15 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 951 5.1 %RANDOM
Rwork0.1967 ---
obs0.19823 17629 99.63 %-
all-17629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.336 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å2-0.53 Å20 Å2
2---1.06 Å20 Å2
3---1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 22 62 2516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222484
X-RAY DIFFRACTIONr_bond_other_d0.0010.022325
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9923362
X-RAY DIFFRACTIONr_angle_other_deg0.71735411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.365325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10524.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16515436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231514
X-RAY DIFFRACTIONr_chiral_restr0.0570.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022753
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02452
X-RAY DIFFRACTIONr_nbd_refined0.1980.2511
X-RAY DIFFRACTIONr_nbd_other0.1630.22317
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21272
X-RAY DIFFRACTIONr_nbtor_other0.080.21465
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.280
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1260.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0640.21
X-RAY DIFFRACTIONr_mcbond_it0.2721.51606
X-RAY DIFFRACTIONr_mcbond_other0.051.5677
X-RAY DIFFRACTIONr_mcangle_it0.5322581
X-RAY DIFFRACTIONr_scbond_it0.8833891
X-RAY DIFFRACTIONr_scangle_it1.5094.5781
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 66 -
Rwork0.238 1254 -
obs-1254 97.92 %
Refinement TLS params.Method: refined / Origin x: -17.6753 Å / Origin y: -70.1772 Å / Origin z: -20.1978 Å
111213212223313233
T-0.1911 Å20.1489 Å2-0.0612 Å2--0.0229 Å2-0.0999 Å2---0.128 Å2
L2.9715 °2-0.0306 °2-0.2122 °2-2.0612 °20.1766 °2--2.0035 °2
S-0.0438 Å °-0.5148 Å °0.3265 Å °0.2732 Å °0.2005 Å °-0.3553 Å °-0.1522 Å °0.1058 Å °-0.1567 Å °

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