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- PDB-9c4l: Crystal structure of mutant NonPro1 Tautomerase Superfamily Membe... -

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Basic information

Entry
Database: PDB / ID: 9c4l
TitleCrystal structure of mutant NonPro1 Tautomerase Superfamily Member NJ7-V1P in complex with 3-bromopropiolate inhibitor
ComponentsAlr4568 protein
KeywordsISOMERASE/INHIBITOR / Tautomerase Superfamily Inhibitor Enzyme MSAD-like / ISOMERASE / ISOMERASE-INHIBITOR complex
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Tautomerase/MIF superfamily / : / Alr4568 protein
Function and homology information
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 4, 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: Alr4568 protein
B: Alr4568 protein
C: Alr4568 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7456
Polymers45,2443
Non-polymers5013
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-19 kcal/mol
Surface area14900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.894, 137.894, 41.076
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z

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Components

#1: Protein Alr4568 protein


Mass: 15081.448 Da / Num. of mol.: 3 / Mutation: V1P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Gene: alr4568 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YNJ7
#2: Chemical ChemComp-A1AWY / 3-bromo-3-oxopropanoic acid


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


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Ammonium Acetate, 0.1M trisodium citrate pH 5.6, 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.09→45.14 Å / Num. obs: 25977 / % possible obs: 97.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.5 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.071 / Rsym value: 0.146 / Net I/σ(I): 10.8
Reflection shellResolution: 2.09→2.17 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2455 / CC1/2: 0.9 / Rpim(I) all: 0.233 / Rsym value: 0.444 / % possible all: 93.5

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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: 2.09→45.14 Å / SU ML: 0.1938 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.8271
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2311 1987 7.65 %
Rwork0.1716 23990 -
obs0.176 25977 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.78 Å2
Refinement stepCycle: LAST / Resolution: 2.09→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 0 18 218 3362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00773212
X-RAY DIFFRACTIONf_angle_d0.91854325
X-RAY DIFFRACTIONf_chiral_restr0.0585475
X-RAY DIFFRACTIONf_plane_restr0.0094547
X-RAY DIFFRACTIONf_dihedral_angle_d13.7214413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.140.27311330.21121604X-RAY DIFFRACTION91.42
2.14-2.20.2781360.18791657X-RAY DIFFRACTION95.58
2.2-2.270.23861380.18061703X-RAY DIFFRACTION96.49
2.27-2.340.26371410.16891709X-RAY DIFFRACTION98.2
2.34-2.420.24321460.17261725X-RAY DIFFRACTION98.63
2.42-2.520.26911450.18171731X-RAY DIFFRACTION98.79
2.52-2.640.2681440.1741709X-RAY DIFFRACTION98.04
2.64-2.780.22771450.17641750X-RAY DIFFRACTION99.06
2.78-2.950.2571410.17621737X-RAY DIFFRACTION99
2.95-3.180.21991410.16911749X-RAY DIFFRACTION99.06
3.18-3.50.22441450.16631731X-RAY DIFFRACTION97.71
3.5-40.2131440.15251707X-RAY DIFFRACTION96.51
4-5.040.19621360.14851667X-RAY DIFFRACTION92.7
5.05-45.140.20941520.19451811X-RAY DIFFRACTION97.56

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