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- PDB-3dkw: Crystal Structure of DNR from Pseudomonas aeruginosa. -

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Basic information

Entry
Database: PDB / ID: 3dkw
TitleCrystal Structure of DNR from Pseudomonas aeruginosa.
ComponentsDNR protein
KeywordsTRANSCRIPTION REGULATOR / CRP-FNR / HTH / beta barrel / dimerization helix / homodimer
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsGiardina, G.
CitationJournal: Proteins / Year: 2009
Title: A dramatic conformational rearrangement is necessary for the activation of DNR from Pseudomonas aeruginosa. Crystal structure of wild-type DNR.
Authors: Giardina, G. / Rinaldo, S. / Castiglione, N. / Caruso, M. / Cutruzzola, F.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNR protein
B: DNR protein
C: DNR protein
D: DNR protein
E: DNR protein
F: DNR protein
G: DNR protein
H: DNR protein
I: DNR protein
J: DNR protein


Theoretical massNumber of molelcules
Total (without water)259,65810
Polymers259,65810
Non-polymers00
Water0
1
A: DNR protein
B: DNR protein


Theoretical massNumber of molelcules
Total (without water)51,9322
Polymers51,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-24 kcal/mol
Surface area25660 Å2
MethodPISA
2
C: DNR protein
D: DNR protein


Theoretical massNumber of molelcules
Total (without water)51,9322
Polymers51,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-19 kcal/mol
Surface area25950 Å2
MethodPISA
3
E: DNR protein
F: DNR protein


Theoretical massNumber of molelcules
Total (without water)51,9322
Polymers51,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-19 kcal/mol
Surface area25720 Å2
MethodPISA
4
G: DNR protein
H: DNR protein


Theoretical massNumber of molelcules
Total (without water)51,9322
Polymers51,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-24 kcal/mol
Surface area26340 Å2
MethodPISA
5
I: DNR protein
J: DNR protein


Theoretical massNumber of molelcules
Total (without water)51,9322
Polymers51,9322
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-22 kcal/mol
Surface area26160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.282, 121.466, 82.554
Angle α, β, γ (deg.)90.00, 97.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
DNR protein / Transcriptional regulator Dnr


Mass: 25965.803 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dnr, PA0527 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q51441

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 20% PEG 3350, 0.2M NH4 Tartrate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 3, 2008 / Details: mirrors
RadiationMonochromator: Single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 3.6→100 Å / Num. all: 27898 / Num. obs: 27033 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 6.7
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3955 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z69

2z69


Resolution: 3.6→100 Å / Cor.coef. Fo:Fc: 0.778 / Cor.coef. Fo:Fc free: 0.721 / SU B: 63.068 / SU ML: 1.019 / Cross valid method: THROUGHOUT / ESU R Free: 1.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.37428 1359 5 %RANDOM
Rwork0.32575 ---
obs0.32819 25660 96.67 %-
all-27019 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.494 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å20 Å21.33 Å2
2---3.19 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 3.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18250 0 0 0 18250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.02115178
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.2541.95320721
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.74952088
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.09524.286546
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.546151870
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.4741545
X-RAY DIFFRACTIONr_chiral_restr0.0180.22501
X-RAY DIFFRACTIONr_gen_planes_refined00.0211589
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2910.26429
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3160.210919
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4550.293
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.6241.510830
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it16.202216453
X-RAY DIFFRACTIONr_scbond_it22.93734813
X-RAY DIFFRACTIONr_scangle_it30.8724.54268
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 96 -
Rwork0.305 1871 -
obs--97.28 %

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