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- PDB-7e85: SnoaL-like domain-containing protein -

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Basic information

Entry
Database: PDB / ID: 7.0E+85
TitleSnoaL-like domain-containing protein
ComponentsSnoaL-like domain-containing protein
KeywordsUNKNOWN FUNCTION / SnoaL-like domain-containing protein / hypothetical protein
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.424 Å
AuthorsZhuang, J.
CitationJournal: To Be Published
Title: SnoaL-like domain-containing protein
Authors: Zhuang, J.
History
DepositionMar 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: SnoaL-like domain-containing protein
A: SnoaL-like domain-containing protein
B: SnoaL-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)39,5423
Polymers39,5423
Non-polymers00
Water3,441191
1
C: SnoaL-like domain-containing protein
A: SnoaL-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,3612
Polymers26,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-15 kcal/mol
Surface area10930 Å2
MethodPISA
2
B: SnoaL-like domain-containing protein

B: SnoaL-like domain-containing protein


Theoretical massNumber of molelcules
Total (without water)26,3612
Polymers26,3612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_444-y-1/4,-x-1/4,-z-1/41
Buried area1780 Å2
ΔGint-17 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.798, 147.798, 147.798
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein SnoaL-like domain-containing protein


Mass: 13180.716 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: Rv3768 / Production host: Escherichia coli (E. coli) / References: UniProt: P72035
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 3.4 Å3/Da / Density % sol: 63.84 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium acetate hydrate (pH 5.2), 2.4M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.42→28.99 Å / Num. obs: 21425 / % possible obs: 99.5 % / Redundancy: 1 % / CC1/2: 0.939 / Net I/σ(I): 16.9
Reflection shellResolution: 2.42→2.52 Å / Num. unique obs: 2215 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.424→28.986 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 1065 4.97 %
Rwork0.2014 20357 -
obs0.204 21422 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.42 Å2 / Biso mean: 53.676 Å2 / Biso min: 24 Å2
Refinement stepCycle: final / Resolution: 2.424→28.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 0 191 2882
Biso mean---49.19 -
Num. residues----342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.424-2.53410.31200.2242497100
2.5341-2.66770.25431280.22022503100
2.6677-2.83470.32421570.23262490100
2.8347-3.05330.28891380.22462506100
3.0533-3.36020.24941340.20482537100
3.3602-3.84540.271420.18532539100
3.8454-4.84120.21041160.17842606100
4.8412-28.9860.25061300.2074267997

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