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- PDB-8t9q: Crystal structure of fused YR, an asymmetric 4-OT trimer -

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Basic information

Entry
Database: PDB / ID: 8t9q
TitleCrystal structure of fused YR, an asymmetric 4-OT trimer
ComponentsTautomerase
KeywordsISOMERASE / 4-OT / trimer / fused
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / Tautomerase/MIF superfamily / isomerase activity / 4-oxalocrotonate tautomerase-like domain-containing protein / 4-oxalocrotonate tautomerase-like domain-containing protein
Function and homology information
Biological speciesHerbaspirillum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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
B: Tautomerase
C: Tautomerase


Theoretical massNumber of molelcules
Total (without water)46,3513
Polymers46,3513
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-30 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.090, 49.409, 49.324
Angle α, β, γ (deg.)102.36, 102.16, 102.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tautomerase


Mass: 15450.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum (bacteria) / Gene: PMI40_00696, PMI40_00695 / Production host: Escherichia coli (E. coli) / References: UniProt: J2VT77, UniProt: J3HY51
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: fYR-4OT was crystallized in 1.5-2M (NH4)2SO4, 0.1M HEPES buffer (pH 7.2-8.0), and 2% PEG 400

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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 6M / Detector: PIXEL / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 18084 / % possible obs: 96 % / Redundancy: 2 % / Rsym value: 0.04 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.3420.2749290.8860.9690.2560.3760.49996.2
2.34-2.382.10.2819170.8070.9450.2570.3820.49795.8
2.38-2.4320.2378560.8410.9560.220.3240.58495.1
2.43-2.4820.2379450.8480.9580.2210.3250.62296.3
2.48-2.531.90.1788680.9130.9770.1640.2430.6696
2.53-2.591.90.1519570.9280.9810.1390.2060.74496.4
2.59-2.6620.1338440.950.9870.1220.1810.70895.3
2.66-2.731.90.1189280.9540.9880.1080.160.72895.6
2.73-2.8120.1018730.9680.9920.0950.1390.87496.3
2.81-2.92.10.0949430.9680.9920.0880.1290.79596.1
2.9-320.0888500.970.9920.0810.121.09596.4
3-3.1220.0689600.9830.9960.0630.0931.15296.8
3.12-3.261.90.0639090.9830.9960.0590.0871.39997.1
3.26-3.4420.0559060.9850.9960.0510.0751.37897.2
3.44-3.651.90.0559010.9860.9970.0510.0751.71696.5
3.65-3.932.10.0488950.9880.9970.0440.0651.48896.7
3.93-4.3320.0488960.9850.9960.0450.0661.77393.8
4.33-4.951.90.0448880.9880.9970.040.061.69294.5
4.95-6.2420.0439170.9890.9970.040.0591.44396.5
6.24-5020.049020.9930.9980.0370.0541.45596.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000v723data scaling
HKL-2000v723data reduction
REFMAC5.8.0267phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→46.51 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.459 / SU ML: 0.249 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30333 1828 10.1 %RANDOM
Rwork0.26929 ---
obs0.27274 16254 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.836 Å2
Baniso -1Baniso -2Baniso -3
1--18.7 Å22.69 Å2-3.47 Å2
2--25.36 Å24.87 Å2
3----6.66 Å2
Refinement stepCycle: 1 / Resolution: 2.29→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 0 32 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132549
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152521
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6363474
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5695790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5735339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36324.286105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.93215408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4881511
X-RAY DIFFRACTIONr_chiral_restr0.0690.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022878
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02504
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.1817.1821374
X-RAY DIFFRACTIONr_mcbond_other7.1837.181373
X-RAY DIFFRACTIONr_mcangle_it9.89510.7771707
X-RAY DIFFRACTIONr_mcangle_other9.89210.7791708
X-RAY DIFFRACTIONr_scbond_it6.8617.6151175
X-RAY DIFFRACTIONr_scbond_other6.8587.6161176
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.82911.2461768
X-RAY DIFFRACTIONr_long_range_B_refined17.5769985
X-RAY DIFFRACTIONr_long_range_B_other17.5789982
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.294→2.353 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 96 -
Rwork0.417 1000 -
obs--76.7 %

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