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- PDB-7mq2: C9A Streptococcus pneumoniae CstR in the reduced state, space gro... -

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Basic information

Entry
Database: PDB / ID: 7mq2
TitleC9A Streptococcus pneumoniae CstR in the reduced state, space group P21
ComponentsCopper-sensing transcriptional repressor csoR
KeywordsTRANSCRIPTION / transcriptional regulator / persulfide sensor / CsoR family / CstR family
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: 2.29 Å
AuthorsFakhoury, J.N. / 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)R35 GM118157-02 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 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Copper-sensing transcriptional repressor csoR
A: Copper-sensing transcriptional repressor csoR
B: Copper-sensing transcriptional repressor csoR
C: Copper-sensing transcriptional repressor csoR


Theoretical massNumber of molelcules
Total (without water)39,3284
Polymers39,3284
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-65 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.440, 45.570, 64.950
Angle α, β, γ (deg.)90.000, 112.848, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 9831.981 Da / Num. of mol.: 4 / Mutation: C9A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, PEG 200 34-40%

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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: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.29→45.57 Å / Num. obs: 14665 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 48.39 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Rsym value: 0.069 / Net I/σ(I): 16.2
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1408 / CC1/2: 0.811 / Rpim(I) all: 0.374 / Rrim(I) all: 0.988 / Rsym value: 0.925 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→36.26 Å / SU ML: 0.3516 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 34.8125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2976 1546 5.48 %
Rwork0.258 26666 -
obs0.2602 14654 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.24 Å2
Refinement stepCycle: LAST / Resolution: 2.29→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 0 0 21 2314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01462305
X-RAY DIFFRACTIONf_angle_d1.75363089
X-RAY DIFFRACTIONf_chiral_restr0.0729379
X-RAY DIFFRACTIONf_plane_restr0.0116398
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.32821160.32252454X-RAY DIFFRACTION99.84
2.36-2.450.41171220.29492412X-RAY DIFFRACTION99.88
2.45-2.550.33671480.29512436X-RAY DIFFRACTION99.81
2.55-2.660.3411070.28722494X-RAY DIFFRACTION99.85
2.66-2.80.31241520.2782360X-RAY DIFFRACTION99.84
2.8-2.980.33941750.29862405X-RAY DIFFRACTION99.73
2.98-3.210.28981960.27492354X-RAY DIFFRACTION99.84
3.21-3.530.30071610.26012433X-RAY DIFFRACTION100
3.53-4.040.3141200.2372440X-RAY DIFFRACTION99.81
4.04-5.090.24241320.23382421X-RAY DIFFRACTION99.8
5.09-36.260.29791170.24942457X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: -7.94626244153 Å / Origin y: 18.572731771 Å / Origin z: -14.1342028241 Å
111213212223313233
T0.445726715047 Å20.0100185461074 Å20.109815223309 Å2-0.184081676351 Å20.00381446035874 Å2--0.569400857322 Å2
L2.89156654704 °2-0.255035268237 °2-0.408959306252 °2-0.73902431755 °2-0.0899624770391 °2--1.50600269094 °2
S0.052172406927 Å °0.23989866554 Å °-0.123105156831 Å °0.150964756036 Å °-0.158371781514 Å °-0.0605366576208 Å °-0.0361807574801 Å °0.212753185137 Å °0.119144672192 Å °
Refinement TLS groupSelection details: all

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