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- PDB-3abf: Crystal Structure of a 4-Oxalocrotonate Tautomerase Homologue (TT... -

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Basic information

Entry
Database: PDB / ID: 3abf
TitleCrystal Structure of a 4-Oxalocrotonate Tautomerase Homologue (TTHB242)
Components4-oxalocrotonate tautomerase
KeywordsISOMERASE / tautomerase
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / isomerase activity / 2-Layer Sandwich / Alpha Beta / 4-oxalocrotonate tautomerase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKida, H. / Miki, K.
CitationJournal: To be Published
Title: Crystal Structure of a 4-Oxalocrotonate Tautomerase Homologue (TTHB242) from Thermus thermophilus HB8
Authors: Kida, H. / Kita, A. / Miki, K.
History
DepositionDec 10, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-oxalocrotonate tautomerase
B: 4-oxalocrotonate tautomerase
C: 4-oxalocrotonate tautomerase
D: 4-oxalocrotonate tautomerase
E: 4-oxalocrotonate tautomerase
F: 4-oxalocrotonate tautomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8489
Polymers44,5606
Non-polymers2883
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13810 Å2
ΔGint-52 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.227, 70.676, 89.906
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
4-oxalocrotonate tautomerase


Mass: 7426.663 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHB242 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53WI4, oxaloacetate tautomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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: 1.97 Å3/Da / Density % sol: 37.53 %
Crystal growTemperature: 290 K / pH: 5.6
Details: 0.6M MgSO4, 0.1M sodium citrate pH 5.6, vapor diffusion, sitting drop, temperature 290K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Oct 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 26856 / % possible obs: 99.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Χ2: 1 / Net I/σ(I): 22.231
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.94-2.013.80.2922605198.3
2.01-2.094.10.22626491100
2.09-2.184.10.17726531100
2.18-2.34.10.1426621100
2.3-2.444.10.10826551100
2.44-2.634.10.09126771100
2.63-2.94.10.0692675199.9
2.9-3.324.10.0512698199.9
3.32-4.1840.0422725199.9
4.18-503.80.0372857198.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJP

1bjp


Resolution: 1.94→43.52 Å / Occupancy max: 1 / Occupancy min: 0
RfactorNum. reflection% reflection
Rfree0.228 1371 5.1 %
Rwork0.193 --
obs0.193 26662 99.7 %
Solvent computationBsol: 67.79 Å2
Displacement parametersBiso mean: 33.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.664 Å20 Å20 Å2
2---1.109 Å20 Å2
3---1.774 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 15 195 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
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_deg
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_it4.2651.5
X-RAY DIFFRACTIONc_mcangle_it5.4372
X-RAY DIFFRACTIONc_scbond_it6.7632
X-RAY DIFFRACTIONc_scangle_it9.0552.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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