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- PDB-8tx9: Nan Regulatory Protein (core isomerase domain) from Streptococcus... -

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Basic information

Entry
Database: PDB / ID: 8tx9
TitleNan Regulatory Protein (core isomerase domain) from Streptococcus pneumoniae
ComponentsMurR/RpiR family 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 / MurR/RpiR family transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsWood, D.M. / Horne, C.R. / Panjikar, S. / 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
Revision 1.1Oct 16, 2024Group: Structure summary / Category: 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
A: MurR/RpiR family transcriptional regulator
C: MurR/RpiR family transcriptional regulator
D: MurR/RpiR family transcriptional regulator
B: MurR/RpiR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,13312
Polymers130,8364
Non-polymers1,2978
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-121 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.577, 147.577, 82.311
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
MurR/RpiR family transcriptional regulator


Mass: 32709.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A064C3N8
#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.: 4 / Source method: obtained synthetically / Formula: C8H16NO9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-ManpNAc6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.72 Å3/Da / Density meas: 7.27696 Mg/m3 / Density % sol: 28.44 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100mM MES pH 6.5, 12% PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953649 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 27, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953649 Å / Relative weight: 1
ReflectionResolution: 2.01→46.67 Å / Num. obs: 58739 / % possible obs: 99.7 % / Redundancy: 13.5 % / Biso Wilson estimate: 44.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.1
Reflection shellResolution: 2.01→2.06 Å / Num. unique obs: 4202 / CC1/2: 0.769

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Processing

Software
NameVersionClassification
REFMAC8.0.013refinement
PHENIX1.20.1_4487refinement
XDS20171111data reduction
Aimless7.0.076data scaling
PHASER7.0.076phasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→42.23 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2707 5588 4.85 %
Rwork0.2106 109682 -
obs0.2134 58739 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.85 Å2
Refinement stepCycle: LAST / Resolution: 2.01→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5985 0 80 184 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01536176
X-RAY DIFFRACTIONf_angle_d1.48798358
X-RAY DIFFRACTIONf_chiral_restr0.0737960
X-RAY DIFFRACTIONf_plane_restr0.03571056
X-RAY DIFFRACTIONf_dihedral_angle_d9.0494825
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.030.47521870.4053199X-RAY DIFFRACTION89.2
2.03-2.060.38852140.35653694X-RAY DIFFRACTION100
2.06-2.080.40072060.3683686X-RAY DIFFRACTION100
2.08-2.110.41691810.34793671X-RAY DIFFRACTION99.97
2.11-2.140.37721860.33333630X-RAY DIFFRACTION100
2.14-2.160.39811460.32263756X-RAY DIFFRACTION100
2.16-2.20.33362110.29823633X-RAY DIFFRACTION100
2.2-2.230.31852060.29413617X-RAY DIFFRACTION100
2.23-2.260.3231780.29073691X-RAY DIFFRACTION100
2.26-2.30.33132300.28873652X-RAY DIFFRACTION99.97
2.3-2.340.32242180.28053646X-RAY DIFFRACTION100
2.34-2.380.28642220.27493617X-RAY DIFFRACTION99.97
2.38-2.430.37451760.28623653X-RAY DIFFRACTION100
2.43-2.480.3752040.27923659X-RAY DIFFRACTION100
2.48-2.530.29841580.25433685X-RAY DIFFRACTION99.95
2.53-2.590.31281680.26563729X-RAY DIFFRACTION99.97
2.59-2.660.31942040.263644X-RAY DIFFRACTION100
2.66-2.730.28282100.25893669X-RAY DIFFRACTION100
2.73-2.810.30711480.2543730X-RAY DIFFRACTION100
2.81-2.90.3282100.26183610X-RAY DIFFRACTION100
2.9-30.38261630.25323698X-RAY DIFFRACTION100
3-3.120.31591800.25413694X-RAY DIFFRACTION100
3.12-3.260.2931540.23083685X-RAY DIFFRACTION100
3.26-3.440.27891940.21023701X-RAY DIFFRACTION99.92
3.44-3.650.30171830.20553605X-RAY DIFFRACTION99.87
3.65-3.930.24871680.18253709X-RAY DIFFRACTION99.87
3.93-4.330.23331540.15213717X-RAY DIFFRACTION99.85
4.33-4.950.16571780.15193643X-RAY DIFFRACTION99.87
4.95-6.240.2131700.16263728X-RAY DIFFRACTION99.95
6.24-42.230.20411810.14643631X-RAY DIFFRACTION99.22

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