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- PDB-3gz6: Crystal structure of Shewanella oneidensis NrtR complexed with a ... -

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Basic information

Entry
Database: PDB / ID: 3gz6
TitleCrystal structure of Shewanella oneidensis NrtR complexed with a 27mer DNA
Components
  • (DNA (27-MER)) x 2
  • MutT/nudix family protein
KeywordsDNA BINDING PROTEIN/DNA / DNA binding protein / NUDIX domain / wHTH domain / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


catalytic activity / identical protein binding
Similarity search - Function
: / NrtR DNA-binding winged helix domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...: / NrtR DNA-binding winged helix domain / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional repressor of nicotinamide riboside utilization NrtR
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsHuang, N. / Zhang, H.
CitationJournal: Structure / Year: 2009
Title: Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism
Authors: Huang, N. / De Ingeniis, J. / Galeazzi, L. / Mancini, C. / Korostelev, Y.D. / Rakhmaninova, A.B. / Gelfand, M.S. / Rodionov, D.A. / Raffaelli, N. / Zhang, H.
History
DepositionApr 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 11, 2017Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.6Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MutT/nudix family protein
D: DNA (27-MER)
B: MutT/nudix family protein
C: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1455
Polymers71,1224
Non-polymers231
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9300 Å2
ΔGint-28 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.580, 159.580, 73.067
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein MutT/nudix family protein


Mass: 27267.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: NrtR, SO_1979 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EFJ3
#2: DNA chain DNA (27-MER)


Mass: 8289.383 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (27-MER)


Mass: 8298.396 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O

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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: 3.78 Å3/Da / Density % sol: 67.43 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER
DetectorDate: Apr 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 23259 / % possible obs: 98.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 20.684
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-36.20.478197.9
3-3.126.20.324198
3.12-3.276.20.194198
3.27-3.446.20.156198
3.44-3.656.10.122197.7
3.65-3.946.10.101199.1
3.94-4.336.10.074198.6
4.33-4.966.10.065199.2
4.96-6.2460.067199.4
6.24-505.70.049198.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GZ5

3gz5


Resolution: 2.901→33.217 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.36 / σ(F): 1.37 / Phase error: 25.91 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2472 1199 5.16 %
Rwork0.174 --
obs0.1777 23248 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.27 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso mean: 36.623 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.901→33.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3510 1109 1 73 4693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084873
X-RAY DIFFRACTIONf_angle_d1.3386860
X-RAY DIFFRACTIONf_dihedral_angle_d22.1591883
X-RAY DIFFRACTIONf_chiral_restr0.067779
X-RAY DIFFRACTIONf_plane_restr0.006690
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9011-3.01720.33321250.2272440X-RAY DIFFRACTION98
3.0172-3.15440.29121400.20442391X-RAY DIFFRACTION98
3.1544-3.32060.29011430.18512421X-RAY DIFFRACTION98
3.3206-3.52840.28511160.17592433X-RAY DIFFRACTION99
3.5284-3.80050.23221290.16222459X-RAY DIFFRACTION99
3.8005-4.18230.20951470.14142428X-RAY DIFFRACTION99
4.1823-4.7860.20361330.12462448X-RAY DIFFRACTION99
4.786-6.02390.20091370.1422500X-RAY DIFFRACTION99
6.0239-33.21930.23781290.19062529X-RAY DIFFRACTION99

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