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- PDB-8t9o: Crystal structure of CF, a heterohexamer of the 4-oxalocrotonate ... -

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Basic information

Entry
Database: PDB / ID: 8t9o
TitleCrystal structure of CF, a heterohexamer of the 4-oxalocrotonate tautomerase (4-OT) family
Components
  • Tautomerase alpha subunit
  • Tautomerase beta subunit
KeywordsISOMERASE / 4-OT / heterohexamer / asymmetric
Function / homologyIsomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups / 4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily / isomerase activity / Tautomerase / 4-oxalocrotonate tautomerase-like domain-containing protein
Function and homology information
Biological speciesHerbaspirillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMoreno, R.Y. / Zhang, Y.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-104896 United States
CitationJournal: Biochemistry / Year: 2023
Title: Introduction of Asymmetry in the Fused 4-Oxalocrotonate Tautomerases.
Authors: Erwin, K. / Moreno, R.Y. / Baas, B.J. / Zhang, Y.J. / Whitman, C.P.
History
DepositionJun 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tautomerase beta subunit
B: Tautomerase alpha subunit
C: Tautomerase alpha subunit
D: Tautomerase alpha subunit
E: Tautomerase beta subunit
F: Tautomerase beta subunit
G: Tautomerase beta subunit
H: Tautomerase beta subunit
I: Tautomerase alpha subunit
J: Tautomerase alpha subunit
K: Tautomerase alpha subunit
L: Tautomerase beta subunit


Theoretical massNumber of molelcules
Total (without water)88,11512
Polymers88,11512
Non-polymers00
Water1,15364
1
A: Tautomerase beta subunit
B: Tautomerase alpha subunit
C: Tautomerase alpha subunit
D: Tautomerase alpha subunit
E: Tautomerase beta subunit
F: Tautomerase beta subunit


Theoretical massNumber of molelcules
Total (without water)44,0576
Polymers44,0576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-71 kcal/mol
Surface area13870 Å2
MethodPISA
2
G: Tautomerase beta subunit
H: Tautomerase beta subunit
I: Tautomerase alpha subunit
J: Tautomerase alpha subunit
K: Tautomerase alpha subunit
L: Tautomerase beta subunit


Theoretical massNumber of molelcules
Total (without water)44,0576
Polymers44,0576
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13220 Å2
ΔGint-70 kcal/mol
Surface area14910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.751, 87.480, 89.698
Angle α, β, γ (deg.)90.00, 125.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Tautomerase beta subunit


Mass: 7512.564 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum (bacteria) / Gene: PMI16_01242 / Production host: Escherichia coli (E. coli) / References: UniProt: J2M343
#2: Protein
Tautomerase alpha subunit


Mass: 7173.199 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum (bacteria) / Gene: PMI16_01243 / Production host: Escherichia coli (E. coli) / References: UniProt: J3DHL6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.05 Å3/Da / Density % sol: 40.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: The protein was crystallized in 15-25% PEG 3350, 0.1M HEPES buffer (pH 7.0-8.0) and 0.2M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18368 / % possible obs: 95 % / Redundancy: 3.4 % / Rsym value: 0.069 / Net I/σ(I): 5.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.752.40.4267770.7930.9410.3020.5250.55480.7
2.75-2.82.50.4327910.7250.9170.2980.5280.62282.8
2.8-2.852.50.4868120.6440.8850.3390.5960.5386
2.85-2.912.60.4978790.7310.9190.3320.6020.52190.6
2.91-2.972.70.4678600.7060.910.3150.5670.5389.5
2.97-3.042.70.3858730.7690.9330.260.4680.58290.3
3.04-3.123.10.4989130.7250.9170.3210.5970.58296.3
3.12-3.23.50.4659610.7950.9410.2880.550.58199
3.2-3.33.60.4579660.7520.9270.2790.5380.60999.5
3.3-3.43.80.3629710.8750.9660.2150.4230.68199.5
3.4-3.523.70.3479430.8740.9660.2070.4060.71999.5
3.52-3.663.70.2999500.8650.9630.1810.3510.88599.1
3.66-3.833.70.2589500.9190.9790.1540.3010.81999.3
3.83-4.033.70.2269660.9190.9790.1380.2650.98399.1
4.03-4.293.60.159540.9520.9880.0930.1781.04298
4.29-4.623.40.1249170.9790.9950.0780.1481.0995.6
4.62-5.0840.1239810.9830.9960.0710.1420.947100
5.08-5.8140.1119530.9810.9950.0650.1290.85899.2
5.81-7.323.80.0939810.9890.9970.0540.1080.86499
7.32-503.50.0699700.9940.9980.0420.0812.14696.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000v723data scaling
HKL-2000v723data reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→43.74 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 1829 10 %
Rwork0.2126 --
obs0.2184 18289 93.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→43.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5579 0 0 64 5643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075633
X-RAY DIFFRACTIONf_angle_d1.0787597
X-RAY DIFFRACTIONf_dihedral_angle_d15.485774
X-RAY DIFFRACTIONf_chiral_restr0.058924
X-RAY DIFFRACTIONf_plane_restr0.007968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.780.3433950.2655907X-RAY DIFFRACTION66
2.78-2.860.32421230.26081119X-RAY DIFFRACTION82
2.86-2.950.35651380.26371165X-RAY DIFFRACTION88
2.95-3.060.34461460.25651204X-RAY DIFFRACTION90
3.06-3.180.34541250.25621318X-RAY DIFFRACTION97
3.18-3.320.30371590.25291331X-RAY DIFFRACTION99
3.32-3.50.28141430.22371351X-RAY DIFFRACTION99
3.5-3.720.26471550.21781342X-RAY DIFFRACTION99
3.72-4.010.2711450.21571337X-RAY DIFFRACTION99
4.01-4.410.21361490.16581316X-RAY DIFFRACTION97
4.41-5.050.23061470.16561352X-RAY DIFFRACTION98
5.05-6.350.24761550.20331357X-RAY DIFFRACTION99
6.36-43.740.2341490.20291361X-RAY DIFFRACTION97

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