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- PDB-12is: Crystal structure of a SnoaL-like domain-containing protein from ... -

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Basic information

Entry
Database: PDB / ID: 12is
TitleCrystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Zinc Bound)
ComponentsSnoaL-like domain-containing protein
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SnoaL-like domain / Mycobacterium ulcerans
Function / homologyNTF2-like domain superfamily / DI(HYDROXYETHYL)ETHER / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycobacterium ulcerans Agy99 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Zinc Bound)
Authors: Liu, L. / Lovell, S. / Ung, A.R. / Buchko, G.W. / Battaile, K.P.
History
DepositionApr 7, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1434
Polymers16,9361
Non-polymers2073
Water2,090116
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2868
Polymers33,8722
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3_554-x,y,-z-1/21
MethodPISA
Unit cell
Length a, b, c (Å)62.071, 71.662, 56.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-356-

HOH

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 16936.111 Da / Num. of mol.: 1 / Fragment: S2-Y125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans Agy99 (bacteria)
Gene: MUL_2490 / Plasmid: MyulA.17060.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0PR67
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.85 Å3/Da / Density % sol: 33.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 12% 4000, 0.1M sodium acetate pH 4.2, 10mM dihdrogen potassium phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. Liu-S-182 drop CD/4, Puck: PSL-0405, Cryo: 32% PEG 4000, 0.2M sodium acetate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 25, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.31→46.92 Å / Num. obs: 53640 / % possible obs: 92 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.012 / Rrim(I) all: 0.045 / Χ2: 0.97 / Net I/σ(I): 26.4
Reflection shellResolution: 1.31→1.34 Å / % possible obs: 56.7 % / Redundancy: 8.1 % / Rmerge(I) obs: 1.01 / Num. measured all: 10031 / Num. unique obs: 1234 / CC1/2: 0.757 / Rpim(I) all: 0.367 / Rrim(I) all: 1.079 / Χ2: 0.75 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→36.05 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 2761 5.15 %
Rwork0.1491 --
obs0.1503 53640 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→36.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 9 116 1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011146
X-RAY DIFFRACTIONf_angle_d1.0391576
X-RAY DIFFRACTIONf_dihedral_angle_d14.751461
X-RAY DIFFRACTIONf_chiral_restr0.081163
X-RAY DIFFRACTIONf_plane_restr0.012205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.330.3216640.29331517X-RAY DIFFRACTION55
1.33-1.360.268930.24871658X-RAY DIFFRACTION60
1.36-1.380.32631120.22921880X-RAY DIFFRACTION68
1.38-1.410.2608990.21322165X-RAY DIFFRACTION78
1.41-1.440.23961280.20042557X-RAY DIFFRACTION91
1.44-1.480.19871560.18362629X-RAY DIFFRACTION96
1.48-1.510.27431530.18142684X-RAY DIFFRACTION97
1.51-1.550.19631230.14972757X-RAY DIFFRACTION99
1.55-1.60.19811620.15572730X-RAY DIFFRACTION99
1.6-1.650.21141890.13312673X-RAY DIFFRACTION99
1.65-1.710.16591420.13922770X-RAY DIFFRACTION99
1.71-1.780.16591520.13012731X-RAY DIFFRACTION99
1.78-1.860.18191600.15412723X-RAY DIFFRACTION99
1.86-1.960.17451320.12842784X-RAY DIFFRACTION99
1.96-2.080.16561500.13142771X-RAY DIFFRACTION100
2.08-2.240.12911590.12542764X-RAY DIFFRACTION100
2.24-2.470.18411460.14962767X-RAY DIFFRACTION100
2.47-2.820.16261580.15142759X-RAY DIFFRACTION100
2.82-3.550.17111510.15582761X-RAY DIFFRACTION100
3.55-36.050.16681320.14722799X-RAY DIFFRACTION100

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