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- PDB-8t9p: Crystal Structure of YR, a heterohexamer of the 4-oxalocrotonate ... -

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Basic information

Entry
Database: PDB / ID: 8t9p
TitleCrystal Structure of YR, a heterohexamer of the 4-oxalocrotonate tautomerase (4-OT) family
Components
  • Tautomerase alpha subunit
  • Tautomerase beta subunit
KeywordsISOMERASE / tautomerase / heterohexamer / asymmetric / 4-OT
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: 2.04 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

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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


Theoretical massNumber of molelcules
Total (without water)43,8046
Polymers43,8046
Non-polymers00
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-55 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.194, 61.028, 92.141
Angle α, β, γ (deg.)90.00, 123.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tautomerase beta subunit


Mass: 7853.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum (bacteria) / Gene: PMI40_00695 / Production host: Escherichia coli (E. coli) / References: UniProt: J3HY51
#2: Protein Tautomerase alpha subunit


Mass: 6747.567 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Herbaspirillum (bacteria) / Gene: PMI40_00696 / Production host: Escherichia coli (E. coli) / References: UniProt: J2VT77
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: The hhYR-4OT was crystallized in 54-64% 2-methyl-2,4-pentanediol (MPD), 0.1M sodium cacodylate pH 6.8, and 5% polyethylene glycol (PEG) 8000

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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: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. obs: 32458 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rsym value: 0.075 / 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
2.05-2.093.40.50815920.7910.940.3140.60.60199.7
2.09-2.123.40.44516120.8120.9470.2770.5260.63899.6
2.12-2.163.60.42116050.8390.9550.2550.4940.63799.9
2.16-2.213.60.35216260.8920.9710.2120.4120.799.9
2.21-2.263.50.28116320.9240.980.1720.3310.7599.9
2.26-2.313.80.25515950.9340.9830.150.2970.85199.8
2.31-2.373.80.22616350.9480.9870.1330.2630.91399.9
2.37-2.433.70.20516100.9550.9880.1220.240.92399.9
2.43-2.53.60.1815900.9610.990.1090.211199.8
2.5-2.583.50.15516060.9690.9920.0950.1831.21199.8
2.58-2.683.70.13516430.9760.9940.0790.1571.21699.8
2.68-2.783.50.1216240.9770.9940.0730.1411.544100
2.78-2.913.80.1116150.9840.9960.0640.1271.578100
2.91-3.063.80.09816340.9860.9960.0570.1141.9899.9
3.06-3.253.60.08816160.9870.9970.0530.1032.43299.9
3.25-3.513.70.07316320.9910.9980.0430.0852.60899.9
3.51-3.863.60.06416290.9930.9980.0380.0752.65299.9
3.86-4.423.70.05616450.9950.9990.0330.0652.83299.9
4.42-5.563.50.05216360.9940.9990.0320.0612.64199.3
5.56-503.60.04916810.9970.9990.0290.0572.44899.3

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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: 2.04→26.84 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1990 6.13 %
Rwork0.1923 --
obs0.1946 32444 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.04→26.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2984 0 0 172 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083017
X-RAY DIFFRACTIONf_angle_d0.9954093
X-RAY DIFFRACTIONf_dihedral_angle_d13.33430
X-RAY DIFFRACTIONf_chiral_restr0.064499
X-RAY DIFFRACTIONf_plane_restr0.008532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.30431400.26242004X-RAY DIFFRACTION94
2.09-2.140.30711290.24322164X-RAY DIFFRACTION100
2.14-2.210.29231520.23462177X-RAY DIFFRACTION100
2.21-2.280.26091360.21582182X-RAY DIFFRACTION100
2.28-2.360.24841500.19942181X-RAY DIFFRACTION100
2.36-2.450.24641360.21292151X-RAY DIFFRACTION100
2.45-2.570.23921470.20472174X-RAY DIFFRACTION100
2.57-2.70.24191390.20632194X-RAY DIFFRACTION100
2.7-2.870.25731450.21082185X-RAY DIFFRACTION100
2.87-3.090.26711420.21342175X-RAY DIFFRACTION100
3.09-3.40.22981430.1932201X-RAY DIFFRACTION100
3.4-3.890.22991400.18862199X-RAY DIFFRACTION100
3.89-4.90.18291400.15952218X-RAY DIFFRACTION100
4.9-26.840.21371510.17782249X-RAY DIFFRACTION99

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