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- PDB-6xnu: CRYSTAL STRUCTURE OF CBPB PROTEIN (LMO1009) FROM LISTERIA MONOCYT... -

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Basic information

Entry
Database: PDB / ID: 6xnu
TitleCRYSTAL STRUCTURE OF CBPB PROTEIN (LMO1009) FROM LISTERIA MONOCYTOGENES
ComponentsCBS domain-containing protein
KeywordsCYTOSOLIC PROTEIN / c-di-AMP binding protein
Function / homology: / : / CBS domain superfamily / CBS domain / CBS domain / CBS domain-containing protein / Lmo1009 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Mbio / Year: 2020
Title: (p)ppGpp and c-di-AMP Homeostasis Is Controlled by CbpB in Listeria monocytogenes.
Authors: Peterson, B.N. / Young, M.K.M. / Luo, S. / Wang, J. / Whiteley, A.T. / Woodward, J.J. / Tong, L. / Wang, J.D. / Portnoy, D.A.
History
DepositionJul 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS domain-containing protein
B: CBS domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4283
Polymers37,3932
Non-polymers351
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-35 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.260, 71.972, 74.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CBS domain-containing protein / Inosine-5'-monophosphate dehydrogenase


Mass: 18696.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Star / References: UniProt: A0A1D2IWV8, UniProt: Q8Y8A3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.95 Å3/Da / Density % sol: 36.89 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.1 / Details: 0.1 M MES (pH 6.1), and 17% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 37711 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Rrim(I) all: 0.052 / Χ2: 1.675 / Net I/σ(I): 16.4 / Num. measured all: 200768
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.62-1.684.30.39134180.910.2050.4440.61290.8
1.68-1.755.30.35537590.9540.1690.3950.65599.9
1.75-1.825.50.24437420.9760.1150.270.783100
1.82-1.925.50.14437820.9910.0680.161.026100
1.92-2.045.50.09937470.9940.0470.111.371100
2.04-2.25.50.07638090.9950.0360.0841.885100
2.2-2.425.50.06437950.9960.030.0712.12799.9
2.42-2.775.50.05638150.9970.0270.0632.481100
2.77-3.495.30.05138560.9970.0240.0573.22199.8
3.49-505.20.03539880.9980.0170.0392.21398.2

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LQN

3lqn


Resolution: 1.62→43.33 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1996 5.3 %
Rwork0.2004 35652 -
obs0.2015 37648 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.44 Å2 / Biso mean: 34.2025 Å2 / Biso min: 20.62 Å2
Refinement stepCycle: final / Resolution: 1.62→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 1 155 2272
Biso mean--30.19 40.53 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.62-1.660.27711260.25382274240090
1.66-1.70.27361460.2512523266999
1.7-1.750.27911330.262925232656100
1.75-1.810.31571480.237125592707100
1.81-1.870.23591380.215825292667100
1.87-1.950.22941430.202525492692100
1.95-2.040.24181530.19825192672100
2.04-2.150.22681360.201125722708100
2.15-2.280.20331480.200425342682100
2.28-2.460.24771440.203625772721100
2.46-2.70.23831390.211925822721100
2.7-3.090.24061400.216926002740100
3.09-3.90.23221500.187226202770100
3.9-43.330.17571520.18582691284398

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