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- PDB-7q93: Crystal Structure of Agrobacterium tumefaciens NADQ, NAD complex. -

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Basic information

Entry
Database: PDB / ID: 7q93
TitleCrystal Structure of Agrobacterium tumefaciens NADQ, NAD 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NrtR DNA-binding winged helix domain-containing protein
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.19 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 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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)155,9729
Polymers154,9934
Non-polymers9795
Water5,008278
1
A: NADQ transcription factor
B: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6814
Polymers77,4972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-22 kcal/mol
Surface area24820 Å2
MethodPISA
2
C: NADQ transcription factor
D: NADQ transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2915
Polymers77,4972
Non-polymers7953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-31 kcal/mol
Surface area24320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.665, 133.721, 87.795
Angle α, β, γ (deg.)90.000, 101.047, 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 (E. coli) / Strain (production host): BL21 / Variant (production host): MET- / References: UniProt: A9CG24
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Bis-tris-propane, 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.19→86.17 Å / Num. obs: 67319 / % possible obs: 98.7 % / Redundancy: 2 % / Biso Wilson estimate: 41.1 Å2 / CC1/2: 0.984 / CC star: 0.996 / Rmerge(I) obs: 0.06162 / Rrim(I) all: 0.08714 / Net I/σ(I): 10.27
Reflection shellResolution: 2.19→2.268 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4347 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6657 / CC1/2: 0.68 / CC star: 0.9 / Rrim(I) all: 0.6147 / % possible all: 98.27

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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 structure

Resolution: 2.19→86.17 Å / SU ML: 0.302 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2588 3402 5.05 %
Rwork0.2278 63899 -
obs0.2293 67301 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.7 Å2
Refinement stepCycle: LAST / Resolution: 2.19→86.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8756 0 63 278 9097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00219015
X-RAY DIFFRACTIONf_angle_d0.455112180
X-RAY DIFFRACTIONf_chiral_restr0.03761302
X-RAY DIFFRACTIONf_plane_restr0.00351577
X-RAY DIFFRACTIONf_dihedral_angle_d13.51923329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.220.3831300.32362645X-RAY DIFFRACTION99.46
2.22-2.250.38841470.30992642X-RAY DIFFRACTION96.74
2.25-2.290.32571500.29372630X-RAY DIFFRACTION99.71
2.29-2.330.31981260.27882663X-RAY DIFFRACTION98.76
2.33-2.370.3111430.26352640X-RAY DIFFRACTION97.86
2.37-2.410.29311470.25582647X-RAY DIFFRACTION99.5
2.41-2.460.26971520.2482661X-RAY DIFFRACTION97.44
2.46-2.510.29961420.25042659X-RAY DIFFRACTION99.86
2.51-2.560.30831490.24922626X-RAY DIFFRACTION97.81
2.56-2.620.30011420.26822667X-RAY DIFFRACTION99.82
2.62-2.690.29911380.26322649X-RAY DIFFRACTION98.03
2.69-2.760.31961360.2432684X-RAY DIFFRACTION98.81
2.76-2.840.28171360.23922632X-RAY DIFFRACTION98.05
2.84-2.930.26171260.23542720X-RAY DIFFRACTION98.85
2.93-3.040.26211750.23052608X-RAY DIFFRACTION99.5
3.04-3.160.25861310.22552667X-RAY DIFFRACTION98.8
3.16-3.30.27231460.23672684X-RAY DIFFRACTION99.09
3.3-3.480.27781390.2332704X-RAY DIFFRACTION99.48
3.48-3.690.24861400.20492685X-RAY DIFFRACTION99.3
3.69-3.980.2391400.21322650X-RAY DIFFRACTION98.69
3.98-4.380.23141370.2012673X-RAY DIFFRACTION98.49
4.38-5.010.21481440.19652688X-RAY DIFFRACTION98.85
5.01-6.310.24771460.22892682X-RAY DIFFRACTION98.43
6.32-86.170.21581400.2142693X-RAY DIFFRACTION97.76

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