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- PDB-8txl: Nan Regulatory Protein full length mutant R148A -

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Basic information

Entry
Database: PDB / ID: 8txl
TitleNan Regulatory Protein full length mutant R148A
ComponentsPhosphosugar-binding transcriptional regulator
KeywordsTRANSCRIPTION / Regulator / DNA-Binding / flexible-domain
Function / homology
Function and homology information


carbohydrate derivative metabolic process / carbohydrate derivative binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Helix-turn-helix protein RpiR / : / Helix-turn-helix domain, rpiR family / RpiR-type HTH domain profile. / RpiR-like, SIS domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Phosphosugar-binding transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsWood, D.M. / Horne, C.R. / Dobson, R.C.J.
Funding support New Zealand, 2items
OrganizationGrant numberCountry
Royal Society of New ZealandUOC1506 New Zealand
Ministry of Business, Innovation and Employment (New Zealand)UOCX1706 New Zealand
CitationJournal: To Be Published
Title: Structure of isomerase domain of the nan-regulatory protein (NanR) from Streptococcus pneumoniae
Authors: Wood, D.M. / Dobson, R.C.J.
History
DepositionAug 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphosugar-binding transcriptional regulator
B: Phosphosugar-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,80420
Polymers65,1302
Non-polymers1,67518
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7920 Å2
ΔGint-129 kcal/mol
Surface area28440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.758, 104.728, 205.659
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphosugar-binding transcriptional regulator


Mass: 32564.850 Da / Num. of mol.: 2 / Mutation: R148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ybbH_2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A4M6CQT5

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Non-polymers , 8 types, 198 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density meas: 4.812 Mg/m3 / Density % sol: 52.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M Lithium sulfate 0.1 M Sodium acetate 4.5 50 % w/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953732 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 1.82→47.69 Å / Num. obs: 61174 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 39.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 3629 / CC1/2: 0.628 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC8.0.013refinement
PHENIX1.20.1_4487refinement
XDS20161205data reduction
Aimless8.0.013data scaling
MOLREP8.0.012phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→42.34 Å / SU ML: 0.2958 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6249
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 3059 5.01 %
Rwork0.2099 58025 -
obs0.212 61084 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.56 Å2
Refinement stepCycle: LAST / Resolution: 1.82→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 99 180 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01144635
X-RAY DIFFRACTIONf_angle_d1.13636245
X-RAY DIFFRACTIONf_chiral_restr0.0607684
X-RAY DIFFRACTIONf_plane_restr0.0138801
X-RAY DIFFRACTIONf_dihedral_angle_d18.44871723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.850.42181580.3992621X-RAY DIFFRACTION99.86
1.85-1.880.40741560.35142549X-RAY DIFFRACTION99.85
1.88-1.910.33681580.32712606X-RAY DIFFRACTION99.96
1.91-1.950.37961420.312587X-RAY DIFFRACTION99.93
1.95-1.980.31291170.29242626X-RAY DIFFRACTION100
1.98-2.020.35851170.2872659X-RAY DIFFRACTION99.93
2.02-2.070.3251380.28132580X-RAY DIFFRACTION99.96
2.07-2.120.31111480.26852620X-RAY DIFFRACTION99.82
2.12-2.170.33061290.24382615X-RAY DIFFRACTION99.96
2.17-2.230.28721380.22942604X-RAY DIFFRACTION99.85
2.23-2.290.27561490.23512616X-RAY DIFFRACTION99.96
2.29-2.370.31121260.22422633X-RAY DIFFRACTION100
2.37-2.450.29651440.2242624X-RAY DIFFRACTION99.96
2.45-2.550.28671290.22552655X-RAY DIFFRACTION99.96
2.55-2.670.27991430.23562619X-RAY DIFFRACTION99.96
2.67-2.810.30931460.23252618X-RAY DIFFRACTION99.96
2.81-2.980.29781260.23882666X-RAY DIFFRACTION99.96
2.98-3.210.30041330.23872667X-RAY DIFFRACTION99.96
3.21-3.540.27261180.20722674X-RAY DIFFRACTION99.96
3.54-4.050.20491350.18072691X-RAY DIFFRACTION99.96
4.05-5.10.19321520.15652689X-RAY DIFFRACTION99.93
5.1-5.760.2021570.18552806X-RAY DIFFRACTION99.83

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