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- PDB-7q91: Crystal Structure of Agrobacterium tumefaciens NADQ, native form. -

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Basic information

Entry
Database: PDB / ID: 7q91
TitleCrystal Structure of Agrobacterium tumefaciens NADQ, native form.
ComponentsNADQ transcription factor
KeywordsTRANSCRIPTION / NADQ / Transcription factor / ATP / NAD / NUDIX domain / WHTH domain / DNA binding / selenium phasing
Function / homologyNicotinic acid mononucleotide biosynthesis protein / AraR-like, winged helix DNA-binding domain / AraR C-terminal winged HTH domain / NUDIX hydrolase-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / ATP binding / AraR-like winged helix DNA-binding domain-containing protein
Function and homology information
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 Å
AuthorsCianci, M. / Minazzato, G. / Heroux, A. / Raffaelli, N. / Sorci, L. / Gasparrini, M.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of Education Italy
CitationJournal: J.Struct.Biol. / Year: 2022
Title: Bacterial NadQ (COG4111) is a Nudix-like, ATP-responsive regulator of NAD biosynthesis.
Authors: Minazzato, G. / Gasparrini, M. / Heroux, A. / Sernova, N.V. / Rodionov, D.A. / Cianci, M. / Sorci, L. / Raffaelli, N.
History
DepositionNov 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADQ transcription factor
B: NADQ transcription factor
C: NADQ transcription factor
D: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,5155
Polymers153,4924
Non-polymers231
Water5,549308
1
A: NADQ transcription factor
B: NADQ transcription factor


  • defined by author&software
  • Evidence: gel filtration, NADQ dimer
  • 76.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)76,7462
Polymers76,7462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-25 kcal/mol
Surface area25880 Å2
MethodPISA
2
C: NADQ transcription factor
D: NADQ transcription factor
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, NADQ dimer
  • 76.8 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)76,7693
Polymers76,7462
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-30 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.308, 133.339, 86.863
Angle α, β, γ (deg.)90.000, 100.097, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
NADQ transcription factor


Mass: 38373.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu4099 / Plasmid: pET100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CG24
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: reservoir 150 mM di-Sodium DL-malate, pH 7.0, 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.31→44.96 Å / Num. obs: 57031 / % possible obs: 99.63 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.07 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05746 / Rrim(I) all: 0.08126 / Net I/σ(I): 9.34
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4718 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 5677 / CC1/2: 0.571 / CC star: 0.853 / Rrim(I) all: 0.6673 / % possible all: 99.49

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.31→44.21 Å / SU ML: 0.3155 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4728
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 1009 1.77 %
Rwork0.1986 56012 -
obs0.1994 57021 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.72 Å2
Refinement stepCycle: LAST / Resolution: 2.31→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9019 0 1 309 9329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00279221
X-RAY DIFFRACTIONf_angle_d0.537712463
X-RAY DIFFRACTIONf_chiral_restr0.03861330
X-RAY DIFFRACTIONf_plane_restr0.00511630
X-RAY DIFFRACTIONf_dihedral_angle_d13.30283403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.430.30551500.2557962X-RAY DIFFRACTION99.55
2.43-2.580.29421440.24337937X-RAY DIFFRACTION99.63
2.58-2.780.31021430.23448035X-RAY DIFFRACTION99.65
2.78-3.060.24881420.22817967X-RAY DIFFRACTION99.59
3.06-3.510.25751430.20437976X-RAY DIFFRACTION99.74
3.51-4.420.21491430.17168063X-RAY DIFFRACTION99.9
4.42-44.210.21691440.17678072X-RAY DIFFRACTION99.47

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