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- PDB-7mq3: C9A N55A Streptococcus pneumoniae CstR in the reduced state -

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Basic information

Entry
Database: PDB / ID: 7mq3
TitleC9A N55A Streptococcus pneumoniae CstR in the reduced state
ComponentsCopper-sensing transcriptional repressor csoR
KeywordsTRANSCRIPTION / CsoR family / persulfide sensor / DNA binding protein
Function / homologyMetal-sensitive transcriptional repressor / Metal-sensitive repressor, helix protomer superfamily / Metal-sensitive transcriptional repressor / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / Copper-sensing transcriptional repressor csoR
Function and homology information
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsFakhoury, J. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Functional asymmetry and chemical reactivity of CsoR family persulfide sensors.
Authors: Fakhoury, J.N. / Zhang, Y. / Edmonds, K.A. / Bringas, M. / Luebke, J.L. / Gonzalez-Gutierrez, G. / Capdevila, D.A. / Giedroc, D.P.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 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
A: Copper-sensing transcriptional repressor csoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9133
Polymers9,6951
Non-polymers2182
Water1,71195
1
A: Copper-sensing transcriptional repressor csoR
hetero molecules

A: Copper-sensing transcriptional repressor csoR
hetero molecules

A: Copper-sensing transcriptional repressor csoR
hetero molecules

A: Copper-sensing transcriptional repressor csoR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,65412
Polymers38,7814
Non-polymers8738
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9770 Å2
ΔGint-94 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.910, 66.930, 76.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-215-

HOH

21A-292-

HOH

31A-293-

HOH

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Components

#1: Protein Copper-sensing transcriptional repressor csoR / Metal-sensing transcriptional repressor


Mass: 9695.166 Da / Num. of mol.: 1 / Mutation: C9A, N55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Gene: csoR, ERS019420_01408, GM542_04805, SAMEA2335968_01957
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B7LQC0
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#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.: 95 / 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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, CaCl2 50 mM, PEG 200 40-50%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97625 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→29.42 Å / Num. obs: 16441 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 18.87 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Rsym value: 0.047 / Net I/σ(I): 27.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 814 / CC1/2: 0.785 / Rpim(I) all: 0.474 / Rrim(I) all: 1.223 / Rsym value: 1.125 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→29.42 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.9905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2251 823 5.03 %
Rwork0.1999 15545 -
obs0.2012 16368 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 0 1 95 759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004688
X-RAY DIFFRACTIONf_angle_d0.6567927
X-RAY DIFFRACTIONf_chiral_restr0.0304108
X-RAY DIFFRACTIONf_plane_restr0.0032120
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.490.33221260.28192510X-RAY DIFFRACTION98.28
1.49-1.60.25061270.22752554X-RAY DIFFRACTION98.71
1.6-1.760.29961350.21432577X-RAY DIFFRACTION99.85
1.76-2.020.25221470.19832566X-RAY DIFFRACTION99.96
2.02-2.540.21761560.18542611X-RAY DIFFRACTION100
2.54-29.420.20011320.1962727X-RAY DIFFRACTION99.34

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