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- PDB-9pl2: Crystal structure of a SnoaL-like domain-containing protein from ... -

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Basic information

Entry
Database: PDB / ID: 9pl2
TitleCrystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans
ComponentsSnoaL-like domain-containing protein
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SnoaL-like domain
Function / homologyNTF2-like domain superfamily / PHOSPHATE ION / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycobacterium ulcerans Agy99 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 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
Authors: Ung, A.R. / Lovell, S. / Liu, L. / Buchko, G.W. / Battaile, K.P.
History
DepositionJul 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2025Provider: 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
B: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9904
Polymers33,8722
Non-polymers1182
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-30 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.632, 131.167, 33.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-296-

HOH

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 16936.111 Da / Num. of mol.: 2
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.86 Å3/Da / Density % sol: 33.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.8
Details: 8% (w/v) PEG 4K, 0.1M Cit pH 3.8, 10mM potassium dihydrogen phosphate. MyulA.17060.a.A1.PB00143 at 15 mg/mL. plate Liu-S-182 C1 Puck: PSL0114, Cryo: 75% crystallant + 25% PEG 200.

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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: Apr 5, 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: 1.37→43.72 Å / Num. obs: 53934 / % possible obs: 99.5 % / Redundancy: 12.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Χ2: 1.03 / Net I/σ(I): 18 / Num. measured all: 656684
Reflection shellResolution: 1.37→1.39 Å / % possible obs: 92.1 % / Redundancy: 7.6 % / Rmerge(I) obs: 1.079 / Num. measured all: 18480 / Num. unique obs: 2428 / CC1/2: 0.68 / Rpim(I) all: 0.408 / Rrim(I) all: 1.158 / Χ2: 1 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(2.0_5750: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→43.29 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1897 2663 4.94 %
Rwork0.1522 --
obs0.1541 53853 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.37→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 6 254 2190
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082073
X-RAY DIFFRACTIONf_angle_d0.9752842
X-RAY DIFFRACTIONf_dihedral_angle_d16.476778
X-RAY DIFFRACTIONf_chiral_restr0.088305
X-RAY DIFFRACTIONf_plane_restr0.011364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.43141170.43222470X-RAY DIFFRACTION91
1.39-1.420.34831420.31622592X-RAY DIFFRACTION98
1.42-1.450.26461510.22232658X-RAY DIFFRACTION99
1.45-1.480.21541310.16742668X-RAY DIFFRACTION100
1.48-1.520.20691400.13842709X-RAY DIFFRACTION100
1.52-1.550.21641270.13852624X-RAY DIFFRACTION100
1.55-1.60.19861210.15782720X-RAY DIFFRACTION100
1.6-1.640.21671520.17152646X-RAY DIFFRACTION100
1.64-1.70.22591520.17582691X-RAY DIFFRACTION100
1.7-1.760.1941480.1472688X-RAY DIFFRACTION100
1.76-1.830.19441500.13172650X-RAY DIFFRACTION100
1.83-1.910.17351320.12442724X-RAY DIFFRACTION100
1.91-2.010.16961620.12222669X-RAY DIFFRACTION100
2.01-2.140.16651390.13082727X-RAY DIFFRACTION100
2.14-2.30.17231190.12972734X-RAY DIFFRACTION100
2.3-2.530.18931390.13952739X-RAY DIFFRACTION100
2.53-2.90.18191320.15162751X-RAY DIFFRACTION100
2.9-3.650.18171410.14022813X-RAY DIFFRACTION100
3.66-43.290.18291680.1722917X-RAY DIFFRACTION100

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