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- PDB-9c6d: Crystal structure of mutant NonPro1 Tautomerase Superfamily Membe... -

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Basic information

Entry
Database: PDB / ID: 9c6d
TitleCrystal structure of mutant NonPro1 Tautomerase Superfamily Member 8U6-S1P in complex with 3-bromopropiolate inhibitor
ComponentsTautomerase family protein
KeywordsISOMERASE/INHIBITOR / Tautomerase Superfamily Inhibitor Enzyme MSAD-like / ISOMERASE / ISOMERASE-INHIBITOR complex
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Tautomerase/MIF superfamily / : / Tautomerase family protein
Function and homology information
Biological speciesSulfurovum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHardtke, H.A. / Venkat Ramani, M.K. / Zhang, Y.J.
Funding support United States, 2items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-2125 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-26168171 United States
CitationJournal: Biochemistry / Year: 2025
Title: Conversion of Inactive Non-Pro1 Tautomerase Superfamily Members into Active Tautomerases: Analysis of the Pro1 Mutants.
Authors: Lancaster, E.B. / Hardtke, H.A. / Melkonian, T.R. / Venkat Ramani, M. / Johnson Jr., W.H. / Baas, B.J. / Zhang, Y.J. / Whitman, C.P.
History
DepositionJun 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tautomerase family protein
B: Tautomerase family protein
C: Tautomerase family protein
D: Tautomerase family protein
E: Tautomerase family protein
F: Tautomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,69110
Polymers89,0236
Non-polymers6684
Water4,342241
1
A: Tautomerase family protein
B: Tautomerase family protein
C: Tautomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6794
Polymers44,5123
Non-polymers1671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-13 kcal/mol
Surface area14680 Å2
MethodPISA
2
D: Tautomerase family protein
E: Tautomerase family protein
F: Tautomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0136
Polymers44,5123
Non-polymers5013
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-13 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.879, 91.975, 138.948
Angle α, β, γ (deg.)90.000, 96.740, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-218-

HOH

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Components

#1: Protein
Tautomerase family protein


Mass: 14837.212 Da / Num. of mol.: 6 / Mutation: S1P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurovum (bacteria) / Gene: SUN_0947 / Production host: Escherichia coli (E. coli) / References: UniProt: A6Q8U6
#2: Chemical
ChemComp-A1AWY / 3-bromo-3-oxopropanoic acid


Mass: 166.958 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H3BrO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate pH 4.6, 15% PEG 20,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→47.51 Å / Num. obs: 40042 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.063 / Rsym value: 0.096 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3683 / CC1/2: 0.791 / Rpim(I) all: 0.33 / Rsym value: 0.487

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Processing

Software
NameVersionClassification
PHENIXphasing
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.51 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.8352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2531 1991 4.97 %
Rwork0.1965 38051 -
obs0.1994 40042 98.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.71 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5793 0 24 241 6058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095939
X-RAY DIFFRACTIONf_angle_d0.97387934
X-RAY DIFFRACTIONf_chiral_restr0.0567827
X-RAY DIFFRACTIONf_plane_restr0.00941028
X-RAY DIFFRACTIONf_dihedral_angle_d9.7234775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.30161230.26342474X-RAY DIFFRACTION88.15
2.15-2.210.29931420.22782601X-RAY DIFFRACTION96.69
2.21-2.280.27191450.23292710X-RAY DIFFRACTION98.65
2.28-2.350.32111420.22272755X-RAY DIFFRACTION98.6
2.35-2.430.26731410.21852734X-RAY DIFFRACTION98.97
2.43-2.530.28411360.21842699X-RAY DIFFRACTION99.23
2.53-2.650.29971510.22592731X-RAY DIFFRACTION99.21
2.65-2.790.29661430.21882745X-RAY DIFFRACTION99.41
2.79-2.960.29621470.20862749X-RAY DIFFRACTION99.35
2.96-3.190.2881460.21592743X-RAY DIFFRACTION99.52
3.19-3.510.22271420.19022751X-RAY DIFFRACTION99.69
3.51-4.020.22881410.17812775X-RAY DIFFRACTION99.59
4.02-5.060.19751490.1522767X-RAY DIFFRACTION99.76
5.06-47.510.24871430.19372817X-RAY DIFFRACTION99.1

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