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- PDB-7q92: Crystal Structure of Agrobacterium tumefaciens NADQ, ATP complex. -

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Basic information

Entry
Database: PDB / ID: 7q92
TitleCrystal Structure of Agrobacterium tumefaciens NADQ, ATP complex.
ComponentsNADQ transcription factor
KeywordsTRANSCRIPTION / NADQ / Transcription factor / ATP / NAD / NUDIX domain / WHTH domain / DNA binding / selenium phasing
Function / homology
Function and homology information


Nicotinic acid mononucleotide biosynthesis protein / : / NrtR DNA-binding winged helix domain / NUDIX hydrolase-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / NrtR DNA-binding winged helix domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.18 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 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 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: NADQ transcription factor
B: NADQ transcription factor
C: NADQ transcription factor
D: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,79627
Polymers154,9934
Non-polymers1,80323
Water6,648369
1
A: NADQ transcription factor
B: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1447
Polymers77,4972
Non-polymers6475
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-27 kcal/mol
Surface area26590 Å2
MethodPISA
2
C: NADQ transcription factor
D: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,65220
Polymers77,4972
Non-polymers1,15618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-35 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.920, 132.570, 86.850
Angle α, β, γ (deg.)90.000, 100.158, 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: 38748.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Selenated version
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: Atu4099 / Plasmid: pET100 / Cell line (production host): B834(DE3) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): MET- / References: UniProt: A9CG24
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Bis-tris-propane, pH 7.0, 250 mM sodium potassium tartrate, 24 % (w/v) PEG 3400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.18→51.84 Å / Num. obs: 66672 / % possible obs: 99.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.114 / Net I/σ(I): 12.6
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.887 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3335 / CC1/2: 0.696 / Rrim(I) all: 0.964 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: native form

Resolution: 2.18→51.84 Å / SU ML: 0.3326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2694 3386 5.08 %
Rwork0.2298 63281 -
obs0.2318 66667 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.59 Å2
Refinement stepCycle: LAST / Resolution: 2.18→51.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9422 0 83 369 9874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00179706
X-RAY DIFFRACTIONf_angle_d0.432313142
X-RAY DIFFRACTIONf_chiral_restr0.03621391
X-RAY DIFFRACTIONf_plane_restr0.00351718
X-RAY DIFFRACTIONf_dihedral_angle_d12.34193581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.34351510.29782639X-RAY DIFFRACTION99.57
2.21-2.250.38151490.30292581X-RAY DIFFRACTION98.95
2.25-2.280.35311380.31292646X-RAY DIFFRACTION99.86
2.28-2.320.32921190.29812638X-RAY DIFFRACTION98.89
2.32-2.360.34681420.27572604X-RAY DIFFRACTION99.93
2.36-2.40.32361490.26482680X-RAY DIFFRACTION99.68
2.4-2.450.30691440.26632599X-RAY DIFFRACTION99.42
2.45-2.50.30831350.25732625X-RAY DIFFRACTION99.78
2.5-2.550.31281510.25652625X-RAY DIFFRACTION99.46
2.55-2.610.33081470.25982616X-RAY DIFFRACTION99.78
2.61-2.680.3091520.2652625X-RAY DIFFRACTION99.5
2.68-2.750.31361290.26162655X-RAY DIFFRACTION99.54
2.75-2.830.34291410.25512625X-RAY DIFFRACTION99.78
2.83-2.920.31661270.25532638X-RAY DIFFRACTION99.71
2.92-3.030.33461470.25052648X-RAY DIFFRACTION99.89
3.03-3.150.28521420.24192638X-RAY DIFFRACTION99.68
3.15-3.290.26531520.24032615X-RAY DIFFRACTION99.68
3.29-3.460.28511300.22762668X-RAY DIFFRACTION99.68
3.46-3.680.25971240.21462665X-RAY DIFFRACTION99.75
3.68-3.960.23191550.20552623X-RAY DIFFRACTION99.71
3.96-4.360.21771290.20042668X-RAY DIFFRACTION99.68
4.36-4.990.20451480.19062629X-RAY DIFFRACTION99.86
5-6.290.25561470.21822691X-RAY DIFFRACTION99.86
6.29-51.840.22231380.19772640X-RAY DIFFRACTION97.68

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