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

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Basic information

Entry
Database: PDB / ID: 1gyx
TitleThe Crystal Structure of YdcE, a 4-Oxalocrotonate Tautomerase Homologue from Escherichia coli, Confirms the Structural Basis for Oligomer Diversity
ComponentsHYPOTHETICAL PROTEIN YDCEHypothesis
KeywordsISOMERASE / TAUTOMERASE / HYPOTHETICAL PROTEIN / COMPLETE PROTEO
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
BENZOIC ACID / Tautomerase PptA
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.35 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 30, 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 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.page_last / _entity_src_gen.gene_src_strain ..._citation.page_last / _entity_src_gen.gene_src_strain / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4624
Polymers17,1012
Non-polymers3602
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)44.566, 46.525, 75.724
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: (-0.41546, 0.909571, 0.008543), (0.909512, 0.415535, -0.010869), (-0.013436, 0.003255, -0.999904)
Vector: 15.042, -9.666, 19.965)

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Components

#1: Protein HYPOTHETICAL PROTEIN YDCE / Hypothesis / YDCE / B1461


Mass: 8550.729 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: INACTIVATED BY HEPES AND BENZOIC ACID / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET24A+ / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P31992, phenylpyruvate tautomerase
#2: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.87 Å3/Da / Density % sol: 56.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROTEIN: 25MG/ML IN 50MM HEPES, PH 7.3, 4 CELCIUS SITTING DROP: MIX 15UL PROTEIN WITH 5UL 40% SODIUM CITRATE PH 6.5
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: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Oct 15, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.35→25 Å / Num. obs: 35377 / % possible obs: 87.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 24.7
Reflection shellResolution: 1.35→1.39 Å / Redundancy: 1 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 3.8 / % possible all: 33
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 156715
Reflection shell
*PLUS
% possible obs: 33 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.35→25 Å / SU B: 0.104 / SU ML: 0.412 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.052
RfactorNum. reflection% reflectionSelection details
Rfree0.164 979 2.7 %RANDOM
Rwork0.142 ---
obs-35377 87.4 %-
Displacement parametersBiso mean: 8.7 Å2
Refinement stepCycle: LAST / Resolution: 1.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1192 0 24 304 1520
Refinement
*PLUS
Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5
LS refinement shell
*PLUS
Highest resolution: 1.35 Å / Lowest resolution: 1.39 Å / Rfactor Rfree: 0.255 / Num. reflection Rfree: 36 / Rfactor Rwork: 0.226 / Num. reflection Rwork: 1343 / Total num. of bins used: 30

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