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- PDB-9dqn: Nan Regulatory Protein (NanR) - DNA complex from Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 9dqn
TitleNan Regulatory Protein (NanR) - DNA complex from Streptococcus pneumoniae
Components
  • (DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)- ...) x 2
  • Phosphosugar-binding transcriptional regulator
KeywordsTRANSCRIPTION/DNA / Regulator / protein-DNA complex / DNA-Binding / Ligand-bound / Isomerase-Domain / TRANSCRIPTION / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Phosphosugar-binding transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 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: Nan Regulatory Protein (NanR) - DNA complex from Streptococcus pneumoniae (CASP target)
Authors: Wood, D.M. / Dobson, R.C.J. / Horne, C.R.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: 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
C: Phosphosugar-binding transcriptional regulator
D: Phosphosugar-binding transcriptional regulator
B: Phosphosugar-binding transcriptional regulator
H: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
I: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
J: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
K: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,89312
Polymers152,6608
Non-polymers2334
Water181
1
A: Phosphosugar-binding transcriptional regulator
B: Phosphosugar-binding transcriptional regulator
H: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
I: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
hetero molecules


  • defined by author
  • Evidence: SAXS, SAXS of the protein-DNA molecule suggests that homodimeric protein binds DNA as a dimer at physiological conditions, assay for oligomerization, Analytical ultracentrifuge experiments ...Evidence: SAXS, SAXS of the protein-DNA molecule suggests that homodimeric protein binds DNA as a dimer at physiological conditions, assay for oligomerization, Analytical ultracentrifuge experiments suggest that this homodimeric protein binds DNA as a dimer at physiological conditions, assay for oligomerization, The tetramer protein that forms the asymmetric unit in this crystal is the exact same tetramer conformation as a mutant protein (SpNanR Arg148) we first crystallized with DNA, and believe that it is a crystal contact, assay for oligomerization, PDBePISA suggests that the contacts formed between the two protein dimers are not inherently solution based, and the buried surface area does not corrospond to a well-define protein-protein interface
  • 76.6 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)76,5638
Polymers76,3304
Non-polymers2334
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Phosphosugar-binding transcriptional regulator
D: Phosphosugar-binding transcriptional regulator
J: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')
K: DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)76,3304
Polymers76,3304
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.893, 159.393, 171.751
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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Protein , 1 types, 4 molecules ACDB

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


Mass: 32650.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: ybbH, ybbH_1, SAMEA2467332_00633, SAMEA3176123_01518, SAMEA3176126_00944, SAMEA3176127_00886
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4M6CQT5

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DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)- ... , 2 types, 4 molecules HJIK

#2: DNA chain DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')


Mass: 5529.614 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*CP*TP*GP*AP*AP*AP*GP*TP*AP*CP*TP*TP*TP*TP*AP*GP*A)-3')


Mass: 5498.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 5 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: SG1 E3 condition: 0.2 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES 7.5, 30 % v/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: 0.953739 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953739 Å / Relative weight: 1
ReflectionResolution: 2.99→46 Å / Num. obs: 30263 / % possible obs: 92 % / Redundancy: 4.9 % / Biso Wilson estimate: 86.11 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.9
Reflection shellResolution: 2.99→3.13 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4821 / CC1/2: 0.25 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→46 Å / SU ML: 0.4758 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0399
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2598 1522 5.03 %
Rwork0.2121 28741 -
obs0.2145 30263 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.16 Å2
Refinement stepCycle: LAST / Resolution: 2.99→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 1476 14 1 10176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003410507
X-RAY DIFFRACTIONf_angle_d0.562414491
X-RAY DIFFRACTIONf_chiral_restr0.03691625
X-RAY DIFFRACTIONf_plane_restr0.00441615
X-RAY DIFFRACTIONf_dihedral_angle_d21.66844102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.090.42821430.3962808X-RAY DIFFRACTION99.39
3.09-3.20.38641420.30452785X-RAY DIFFRACTION99.29
3.2-3.320.30071650.27972757X-RAY DIFFRACTION99.02
3.32-3.440.36441060.27522145X-RAY DIFFRACTION94.66
3.49-3.660.26181260.23222468X-RAY DIFFRACTION96
3.66-3.890.23291010.21182050X-RAY DIFFRACTION72.23
3.89-4.190.2391240.18412212X-RAY DIFFRACTION78.23
4.19-4.610.23441600.18872813X-RAY DIFFRACTION99.53
4.61-5.280.23841410.18362878X-RAY DIFFRACTION99.31
5.28-6.640.251400.22522857X-RAY DIFFRACTION98.1
6.64-45.960.2391740.1772968X-RAY DIFFRACTION97.58

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