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- PDB-2uyn: Crystal structure of E. coli TdcF with bound 2-ketobutyrate -

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Basic information

Entry
Database: PDB / ID: 2uyn
TitleCrystal structure of E. coli TdcF with bound 2-ketobutyrate
Components(PROTEIN TDCF) x 2
KeywordsUNKNOWN FUNCTION / YJGF/YER057C/UK114 FAMILY / TDCF PROTEIN / LIGAND BINDING / 2-KETOBUTYRATE
Function / homology
Function and homology information


L-threonine catabolic process to propionate / threonine metabolic process / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines / deaminase activity / identical protein binding / cytosol
Similarity search - Function
RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / RutC-like / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-KETOBUTYRIC ACID / Putative reactive intermediate deaminase TdcF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBurman, J.D. / Stevenson, C.E.M. / Sawers, R.G. / Lawson, D.M.
CitationJournal: Bmc Struct.Biol. / Year: 2007
Title: The Crystal Structure of Escherichia Coli Tdcf, a Member of the Highly Conserved Yjgf/Yer057C/Uk114 Family.
Authors: Burman, J.D. / Stevenson, C.E.M. / Sawers, R.G. / Lawson, D.M.
History
DepositionApr 11, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN TDCF
B: PROTEIN TDCF
C: PROTEIN TDCF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5546
Polymers42,2473
Non-polymers3063
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.581, 85.901, 62.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2104-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.20526, 0.8457, -0.4926), (0.63804, 0.26603, 0.72259), (0.74214, -0.46262, -0.48499)2.54196, -6.41493, 22.8266
2given(0.20849, 0.62634, 0.75116), (0.84308, 0.27421, -0.46264), (-0.49574, 0.72974, -0.47088)-13.52896, 9.76452, 16.57689
3given(0.20247, 0.84246, -0.49928), (0.63285, 0.27652, 0.72322), (0.74734, -0.46239, -0.47716)2.75681, -6.57728, 22.60171

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Components

#1: Protein PROTEIN TDCF / TDCF


Mass: 14111.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MC4100 / Plasmid: PETHF1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGL2
#2: Protein PROTEIN TDCF / TDCF


Mass: 14068.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MC4100 / Plasmid: PETHF1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGL2
#3: Chemical ChemComp-2KT / 2-KETOBUTYRIC ACID / 2-OXOBUTANOIC ACID


Mass: 102.089 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.02 Å3/Da / Density % sol: 46.76 %
Crystal growpH: 7 / Details: 10% PEG 1000, 8% PEG 8000, NO BUFFER, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→35.42 Å / Num. obs: 49864 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 17.14 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.67
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.08 / % possible all: 71.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QU9

1qu9


Resolution: 1.6→33.48 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.995 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2577 5.28 %RANDOM
Rwork0.162 ---
obs0.164 49862 95 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.792 Å20 Å20 Å2
2--0.705 Å20 Å2
3---0.087 Å2
Refinement stepCycle: LAST / Resolution: 1.6→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2891 0 21 400 3312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222958
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9794026
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6285378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.2825.583120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315499
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0651513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022205
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21545
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22097
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4481.51956
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99223095
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.33831105
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6634.5931
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 7→33.48 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.2 30
Rwork0.209 616

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