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- PDB-2uyp: Crystal structure of E. coli TdcF with bound propionate -

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Basic information

Entry
Database: PDB / ID: 2uyp
TitleCrystal structure of E. coli TdcF with bound propionate
ComponentsPROTEIN TDCF
KeywordsUNKNOWN FUNCTION / YJGF/YER057C/UK114 FAMILY / 2-KETOBUTYRATE / PROPIONATE / TDCF PROTEIN / LIGAND BINDING
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
PROPANOIC ACID / Putative reactive intermediate deaminase TdcF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 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 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)42,3525
Polymers42,2043
Non-polymers1482
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.435, 85.744, 62.512
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-2035-

HOH

21A-2054-

HOH

31A-2065-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.21144, 0.84524, -0.49077), (0.64947, 0.25373, 0.7168), (0.7304, -0.4703, -0.49531)2.43357, -6.15162, 23.28669
2given(0.21883, 0.63127, 0.74405), (0.8418, 0.26347, -0.47112), (-0.49344, 0.72944, -0.47375)-13.51874, 10.07498, 16.57422
3given(0.21467, 0.8356, -0.50566), (0.63183, 0.27599, 0.7243), (0.74478, -0.47498, -0.46872)2.87474, -6.63494, 22.75538

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Components

#1: Protein PROTEIN TDCF / TDCF


Mass: 14068.104 Da / Num. of mol.: 3
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: Chemical ChemComp-PPI / PROPANOIC ACID


Mass: 74.079 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 46.49 %
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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 11, 2002 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→25.25 Å / Num. obs: 14818 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.49
Reflection shellResolution: 2.45→2.54 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.58 / % possible all: 94

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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: 2.44→24.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.889 / SU B: 7.916 / SU ML: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.541 / ESU R Free: 0.295 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 756 5.12 %RANDOM
Rwork0.166 ---
obs0.171 14817 99.2 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.007 Å20 Å20 Å2
2--0.8 Å20 Å2
3---0.207 Å2
Refinement stepCycle: LAST / Resolution: 2.44→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2860 0 10 195 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222913
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.9743969
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0775379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27825.138109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59415482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2641513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.21416
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22014
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1221.51977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7923098
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.76631058
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3294.5871
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: 10.03→24.58 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 11
Rwork0.24 222

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