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- PDB-6xnv: CRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES CBPB PROTEIN (LMO1009... -

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Basic information

Entry
Database: PDB / ID: 6xnv
TitleCRYSTAL STRUCTURE OF LISTERIA MONOCYTOGENES CBPB PROTEIN (LMO1009) IN COMPLEX WITH C-DI-AMP
ComponentsCBS domain-containing protein
KeywordsCYTOSOLIC PROTEIN / c-di-AMP binding protein
Function / homologyCBS domain superfamily / CBS domain / CBS domain / Chem-2BA / CBS domain-containing protein / Lmo1009 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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)38,7094
Polymers37,3932
Non-polymers1,3172
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-22 kcal/mol
Surface area13890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.934, 61.934, 171.509
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 18696.324 Da / Num. of mol.: 2 / Fragment: residues 12-150
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-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44.07 % / Mosaicity: 0.245 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 8
Details: 200 mM CaCl2, 100 mM imidazole, pH 8.0, 14% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 13591 / % possible obs: 98.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.039 / Rrim(I) all: 0.087 / Χ2: 1.053 / Net I/σ(I): 9 / Num. measured all: 64523
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.494.20.47412500.8270.2450.5360.97392.9
2.49-2.594.60.36713130.8870.1850.4121.08697
2.59-2.74.50.26313090.9420.1330.2961.08498.3
2.7-2.845.10.2113440.9620.10.2331.08599.8
2.84-3.0250.16213530.9760.0780.1811.08899.7
3.02-3.264.70.12113680.9750.0610.1361.08599.2
3.26-3.5850.09913480.9860.0480.111.00899.5
3.58-4.14.90.08213940.990.040.0921.02399.6
4.1-5.164.80.06814110.9910.0340.0771.02499
5.16-254.50.05615010.9940.0290.0641.06697.5

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Processing

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

3lqn


Resolution: 2.4→24.93 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2758 1357 10 %
Rwork0.2108 12211 -
obs0.2172 13568 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.85 Å2 / Biso mean: 64.4257 Å2 / Biso min: 31.42 Å2
Refinement stepCycle: final / Resolution: 2.4→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 88 14 2230
Biso mean--52.31 56.44 -
Num. residues----265
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.490.42441250.30321124124993
2.49-2.590.29571310.25431182131397
2.59-2.70.29011310.24271178130998
2.7-2.840.36141350.255512081343100
2.85-3.020.33671340.258312171351100
3.02-3.260.31361360.22631231136799
3.26-3.580.33051350.217812091344100
3.58-4.10.21911380.195612521390100
4.1-5.150.23511420.18321267140999
5.16-24.930.27141500.20231343149399

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