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- PDB-1gyj: The Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Hom... -

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Basic information

Entry
Database: PDB / ID: 1gyj
TitleThe Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity
ComponentsHYPOTHETICAL PROTEIN YDCE
KeywordsISOMERASE / TAUTOMERASE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


intramolecular oxidoreductase activity, interconverting keto- and enol-groups / Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / protein homodimerization activity / cytoplasm
Similarity search - Function
Tautomerase PptA / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAlmrud, J. / Kern, A. / Wang, S. / Czerwinski, R. / Johnson, W. / Murzin, A. / Hackert, M. / Whitman, C.
CitationJournal: Biochemistry / Year: 2002
Title: The Crystal Structure of Ydce, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia Coli, Confirms the Structural Basis for Oligomer Diversity
Authors: Almrud, J. / Kern, A. / Wang, S. / Czerwinski, R. / Johnson, W. / Murzin, A. / Hackert, M. / Whitman, C.
History
DepositionApr 23, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YDCE
B: HYPOTHETICAL PROTEIN YDCE


Theoretical massNumber of molelcules
Total (without water)17,1012
Polymers17,1012
Non-polymers00
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.250, 63.810, 71.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.161249, -0.963495, 0.213719), (-0.961701, -0.202037, -0.185234), (0.221652, -0.175665, -0.959173)
Vector: -2.40497, 6.35961, 40.75565)

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Components

#1: Protein HYPOTHETICAL PROTEIN YDCE / YDCE / B1461


Mass: 8550.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET24A+ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31992, phenylpyruvate tautomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.3
Details: PROTEIN BUFFERED IN 50MM SODIUM PHOSPHATE, PH 7.3 PRECIPITANT: 40% SODIUM CITRATE PH 8.5 ITTING DROP: MIX 5UL PROT. WITH 5UL 40% SODIUM CITRATE
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
240 %(w/v)sodium citrate1reservoirpH8.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 2001 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 10344 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 16 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 3 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 169053
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.435

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED 1.35 ANG. RES. YDCE STRUCTURE DETERMINED BY MIR

Resolution: 2.1→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.262 491 4.7 %RANDOM
Rwork0.225 ---
obs0.225 10344 99.7 %-
Solvent computationSolvent model: COMBINATION
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.62 Å20 Å20 Å2
2---1.586 Å20 Å2
3---6.206 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 151 1351
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.42
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.1→2.18 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.329 50 4.7 %
Rwork0.302 1017 -
obs--99.1 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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