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- PDB-2z69: Crystal Structure of the sensor domain of the transcriptional reg... -

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Basic information

Entry
Database: PDB / ID: 2z69
TitleCrystal Structure of the sensor domain of the transcriptional regulator DNR from Pseudomonas aeruginosa
ComponentsDNR protein
KeywordsTRANSCRIPTION REGULATOR / beta barrel / dimerization helix
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
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 DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGiardina, G. / Johnson, K.A. / Di Matteo, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: NO sensing in Pseudomonas aeruginosa: structure of the transcriptional regulator DNR.
Authors: Giardina, G. / Rinaldo, S. / Johnson, K.A. / Di Matteo, A. / Brunori, M. / Cutruzzola, F.
History
DepositionJul 24, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNR protein
B: DNR protein
C: DNR protein


Theoretical massNumber of molelcules
Total (without water)52,9173
Polymers52,9173
Non-polymers00
Water1,856103
1
A: DNR protein
B: DNR protein


Theoretical massNumber of molelcules
Total (without water)35,2782
Polymers35,2782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-25.9 kcal/mol
Surface area14850 Å2
MethodPISA
2
C: DNR protein

C: DNR protein


Theoretical massNumber of molelcules
Total (without water)35,2782
Polymers35,2782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3640 Å2
ΔGint-23.5 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.145, 105.534, 74.838
Angle α, β, γ (deg.)90.00, 97.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-187-

HOH

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Components

#1: Protein DNR protein / Transcriptional regulator Dnr / DNR DISSIMILATIVE NITRATE RESPIRATION REGULATOR


Mass: 17639.158 Da / Num. of mol.: 3 / Fragment: Sensor Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dnr / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q51441
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 14% (w/v) PEG 4000, 100mM Sodium Citrate (pH 5.4), 200mM Potassium Fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.1→74.12 Å / Num. all: 23925 / Num. obs: 23925 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.9 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.066 / Net I/σ(I): 11.2
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 6.7 / Num. unique all: 1490 / Rsym value: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 2.1→74.12 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 13.325 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26235 1300 5.2 %RANDOM
Rwork0.21489 ---
obs0.2174 23925 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.102 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.83 Å2
2---0.27 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→74.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3365 0 0 103 3468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223434
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9584669
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.915430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64424.076157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79615538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7391519
X-RAY DIFFRACTIONr_chiral_restr0.1010.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.09822247
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66633466
X-RAY DIFFRACTIONr_scbond_it3.67251333
X-RAY DIFFRACTIONr_scangle_it5.706101203
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 90 -
Rwork0.237 1805 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.78181.8952.62236.10331.33328.5237-0.49120.5776-0.0587-0.75510.33630.2027-0.2720.38160.1549-0.0411-0.08790.02080.0379-0.0121-0.1616-2.8615-37.388918.0486
23.33742.34111.73647.46574.896511.1827-0.66880.54780.4632-1.77190.57460.6921-1.44090.39160.09430.2338-0.2155-0.10550.10810.118-0.0725-4.2716-30.321213.5738
38.0635.9464-7.283317.1745-4.03979.23440.23070.170.1165-0.1270.2128-0.048-0.76510.1342-0.4435-0.0276-0.05970.01660.0421-0.0099-0.04693.9783-23.655627.0887
411.7833-10.156-1.646937.6929-14.585119.47310.4821.3878-1.1343-3.9964-1.2981.28451.4449-0.16720.8160.5928-0.1378-0.24330.33540.03440.22175.5057-5.757617.8185
55.30852.66112.941510.7069-2.22835.76510.5493-1.01490.00841.8201-0.25360.07310.1087-0.5558-0.29570.4843-0.11490.07660.2560.06840.09726.774-6.418844.2462
66.80031.224-1.54376.96830.42997.73620.05990.4609-0.1-0.31310.3328-0.00990.039-0.2185-0.3926-0.1616-0.0310.0166-0.1087-0.001-0.116412.4275.20526.2065
72.72462.79190.08997.0534-1.95923.3580.02460.0959-0.4061-0.0230.12380.13510.4604-0.275-0.1484-0.0569-0.0273-0.0066-0.0210.0053-0.05439.6904-1.092828.9336
83.98693.2463-2.95728.72153.13299.58030.07330.75340.338-0.95190.03970.2574-0.2882-0.2926-0.11290.2529-0.02010.0740.11070.06510.16811.2755-16.747124.693
914.2914-10.1083-1.345517.4577-15.619326.76580.2654-1.3551.7880.8808-0.9134-2.8615-2.16761.49990.6480.2043-0.08260.05430.33190.06490.84183.551434.742116.8055
105.9069-4.94790.06416.821-4.01724.44270.1375-0.0721-0.3891-0.06730.0240.4932-0.0171-0.0218-0.1615-0.10930.04850.00870.16550.03970.0336-5.31921.201919.4445
116.3096-5.5583.489827.2896-10.949717.7650.4295-0.28690.4394-0.5934-0.3482-0.2174-0.6186-0.3655-0.0812-0.01560.10750.040.1065-0.0550.0375-7.063531.708214.5939
121.26751.67091.31272.32430.581612.2184-0.16360.157-0.01271.3980.94051.03151.2029-0.0298-0.77690.59310.09880.28220.41990.13660.29852.014424.95350.1856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 661 - 69
2X-RAY DIFFRACTION2AA67 - 11770 - 120
3X-RAY DIFFRACTION3AA118 - 137121 - 140
4X-RAY DIFFRACTION4AA138 - 150141 - 153
5X-RAY DIFFRACTION5BB1 - 314 - 34
6X-RAY DIFFRACTION6BB32 - 7335 - 76
7X-RAY DIFFRACTION7BB74 - 11877 - 121
8X-RAY DIFFRACTION8BB119 - 150122 - 153
9X-RAY DIFFRACTION9CC7 - 2110 - 24
10X-RAY DIFFRACTION10CC22 - 10725 - 110
11X-RAY DIFFRACTION11CC108 - 120111 - 123
12X-RAY DIFFRACTION12CC121 - 150124 - 153

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