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- PDB-8v4v: Nan Regulatory Protein Full-length from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 8v4v
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
Chem-BMX / Phosphosugar-binding transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 29, 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
B: Phosphosugar-binding transcriptional regulator
A: Phosphosugar-binding transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9867
Polymers65,3022
Non-polymers6845
Water00
1
B: Phosphosugar-binding transcriptional regulator
A: Phosphosugar-binding transcriptional regulator
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)131,97114
Polymers130,6044
Non-polymers1,36810
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445-x-1/2,-y-1/2,z1
Buried area15380 Å2
ΔGint-145 kcal/mol
Surface area38300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.873, 223.646, 52.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
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
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z

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Components

#1: Protein Phosphosugar-binding transcriptional regulator


Mass: 32650.963 Da / Num. of mol.: 2
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: Sugar ChemComp-BMX / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose / 2-(ACETYLAMINO)-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-MANNOPYRANOSE / N-acetyl-6-O-phosphono-alpha-D-mannosamine / 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-D-mannose / 2-acetamido-2-deoxy-6-O-phosphono-mannose


Type: D-saccharide, alpha linking / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-ManpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
Has ligand of interestY
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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 15.5 mg/mL protein + 0.1 M phosphate/citrate, pH 4.2, 40% v/v PEG300 + 10 mM ligand (ManNac-6-P), cryoprotectant: 50:50 ethylene glycol/glycerol

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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: Jul 28, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953732 Å / Relative weight: 1
ReflectionResolution: 2.95→47.7 Å / Num. obs: 15063 / % possible obs: 99.85 % / Redundancy: 8.9 % / Biso Wilson estimate: 70.7 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.2461 / Net I/σ(I): 7.49
Reflection shellResolution: 2.95→3.056 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1478 / CC1/2: 0.355 / CC star: 0.724 / % possible all: 99.93

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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: 2.95→47.7 Å / SU ML: 0.394 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.498
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3013 767 5.1 %
Rwork0.2515 14285 -
obs0.2539 15052 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.93 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 41 0 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00493819
X-RAY DIFFRACTIONf_angle_d0.67265161
X-RAY DIFFRACTIONf_chiral_restr0.0384583
X-RAY DIFFRACTIONf_plane_restr0.015657
X-RAY DIFFRACTIONf_dihedral_angle_d5.1167504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.180.35031950.34522759X-RAY DIFFRACTION99.9
3.18-3.50.32681370.31312835X-RAY DIFFRACTION100
3.5-40.3261440.25072833X-RAY DIFFRACTION99.9
4-5.040.25211580.22012841X-RAY DIFFRACTION99.97
5.04-47.10.30441330.2323017X-RAY DIFFRACTION99.75

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