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

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Basic information

Entry
Database: PDB / ID: 9yaa
TitleCrystal structure of a SnoaL-like domain-containing protein from Mycobacterium ulcerans (Orthorhombic C form)
ComponentsSnoaL-like domain-containing protein
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SnoaL-like domain
Function / homologyNTF2-like domain superfamily / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycobacterium ulcerans Agy99 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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 (Orthorhombic C form)
Authors: Liu, L. / Lovell, S. / Ung, A.R. / Buchko, G.W. / Battaile, K.P.
History
DepositionSep 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1302
Polymers16,9361
Non-polymers1941
Water2,054114
1
A: SnoaL-like domain-containing protein
hetero molecules

A: SnoaL-like domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2614
Polymers33,8722
Non-polymers3882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3140 Å2
ΔGint-4 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.073, 71.564, 56.445
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-362-

HOH

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 16936.111 Da / Num. of mol.: 1
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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.85 Å3/Da / Density % sol: 33.54 %
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-0407, 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: 1.36→46.89 Å / Num. obs: 27166 / % possible obs: 99.2 % / Redundancy: 12.3 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Χ2: 0.95 / Net I/σ(I): 23 / Num. measured all: 334155
Reflection shellResolution: 1.36→1.4 Å / % possible obs: 92.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.814 / Num. measured all: 13108 / Num. unique obs: 1846 / CC1/2: 0.793 / Rpim(I) all: 0.317 / Rrim(I) all: 0.877 / Χ2: 0.7 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5819: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→46.89 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1815 1399 5.15 %
Rwork0.1579 --
obs0.1591 27139 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 13 114 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091093
X-RAY DIFFRACTIONf_angle_d1.0281491
X-RAY DIFFRACTIONf_dihedral_angle_d15.626428
X-RAY DIFFRACTIONf_chiral_restr0.081154
X-RAY DIFFRACTIONf_plane_restr0.012190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.410.26121270.22812375X-RAY DIFFRACTION93
1.41-1.470.2271440.1942518X-RAY DIFFRACTION99
1.47-1.530.24391360.19672585X-RAY DIFFRACTION100
1.53-1.610.1921510.16212542X-RAY DIFFRACTION100
1.61-1.710.18231400.14052590X-RAY DIFFRACTION100
1.71-1.850.17881330.152569X-RAY DIFFRACTION100
1.85-2.030.17421260.14382592X-RAY DIFFRACTION100
2.03-2.330.1891400.14272616X-RAY DIFFRACTION100
2.33-2.930.16641520.16352621X-RAY DIFFRACTION100
2.93-46.890.17841500.15942732X-RAY DIFFRACTION100

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