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- PDB-8v5f: Nan Regulatory Protein Full-length from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 8v5f
TitleNan Regulatory Protein Full-length from Streptococcus pneumoniae
ComponentsPhosphosugar-binding transcriptional regulator
KeywordsTRANSCRIPTION / Regulator / DNA-Binding / Ligand-bound / Isomerase-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
PHOSPHATE ION / Phosphosugar-binding transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsWood, D.M. / Dobson, R.C.J. / Horne, C.R.
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 full-length nan-regulatory protein (NanR) from Streptococcus pneumoniae
Authors: Wood, D.M. / Dobson, R.C.J. / Horne, C.R.
History
DepositionNov 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 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
C: Phosphosugar-binding transcriptional regulator
D: Phosphosugar-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,89120
Polymers130,6044
Non-polymers1,28716
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14580 Å2
ΔGint-228 kcal/mol
Surface area43980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.241, 109.226, 202.385
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Phosphosugar-binding transcriptional regulator / Nan Regulatory protein / NanR


Mass: 32650.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: ybbH_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4M6CQT5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: 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 modificationN

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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: 2.25 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953739 Å / Relative weight: 1
ReflectionResolution: 2.55→45.91 Å / Num. obs: 39440 / % possible obs: 97.63 % / Redundancy: 10.1 % / Biso Wilson estimate: 54.13 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1877 / Net I/σ(I): 9.16
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 0.77 / Num. unique obs: 3859 / CC1/2: 0.61 / CC star: 0.87 / % possible all: 98.01

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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
Starting model: PDB entry 8TX9

8tx9


Resolution: 2.55→45.91 Å / SU ML: 0.4507 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.7238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3128 1898 4.93 %
Rwork0.2615 36623 -
obs0.2641 38521 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.33 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7863 0 64 21 7948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00638057
X-RAY DIFFRACTIONf_angle_d0.82110894
X-RAY DIFFRACTIONf_chiral_restr0.04191218
X-RAY DIFFRACTIONf_plane_restr0.01821396
X-RAY DIFFRACTIONf_dihedral_angle_d5.44321061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.47281330.44252556X-RAY DIFFRACTION97.75
2.61-2.680.46311440.4142595X-RAY DIFFRACTION98.17
2.68-2.760.42731420.36232588X-RAY DIFFRACTION99.78
2.76-2.850.4071340.34912619X-RAY DIFFRACTION98.64
2.85-2.950.39261300.3382642X-RAY DIFFRACTION98.61
2.95-3.070.39371140.34492629X-RAY DIFFRACTION99.35
3.07-3.210.38511090.30682625X-RAY DIFFRACTION98.17
3.21-3.380.38641340.30762627X-RAY DIFFRACTION98.19
3.38-3.590.32051540.2732548X-RAY DIFFRACTION96.78
3.59-3.870.29321390.24792554X-RAY DIFFRACTION95.7
3.87-4.260.28551250.21252639X-RAY DIFFRACTION98.05
4.26-4.880.28121420.19882650X-RAY DIFFRACTION97.01
4.88-6.140.2661410.23372642X-RAY DIFFRACTION97.1
6.14-45.910.2491570.21582709X-RAY DIFFRACTION94.34

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