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- PDB-2rbf: Structure of the ribbon-helix-helix domain of Escherichia coli Pu... -

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Basic information

Entry
Database: PDB / ID: 2rbf
TitleStructure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)
Components
  • Bifunctional protein putA
  • DNA (5'-D(*DTP*DT*DTP*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DCP*DAP*DAP*DA)-3')
  • DNA (5'-D(*DTP*DTP*DTP*DGP*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DAP*DAP*DA)-3')
KeywordsOXIDOREDUCTASE/DNA / Protein-DNA complex / ribbon-helix-helix / proline utilization A / PutA / DNA-binding / FAD / Flavoprotein / Multifunctional enzyme / NAD / Oxidoreductase / Proline metabolism / Repressor / Transcription / Transcription regulation / OXIDOREDUCTASE-DNA COMPLEX
Function / homology
Function and homology information


proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding ...proline dehydrogenase / proline dehydrogenase activity / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / proline biosynthetic process / DNA-binding transcription repressor activity / cis-regulatory region sequence-specific DNA binding / cytoplasmic side of plasma membrane / flavin adenine dinucleotide binding / response to oxidative stress / sequence-specific DNA binding / negative regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like ...: / PutA, RHH domain / Proline dehydrogenase PutA, domain I / Proline utilization A proline dehydrogenase N-terminal domain / Proline utilization A proline dehydrogenase N-terminal domain / Delta-1-pyrroline-5-carboxylate dehydrogenase 3 / Proline dehydrogenase PutA, domain II / Proline dehydrogenase PutA, domain I/II / DNA-binding domain of Proline dehydrogenase / Met repressor-like / Bifunctional protein PutA / Proline dehydrogenase domain / Proline dehydrogenase / Arc Repressor Mutant / FAD-linked oxidoreductase-like / Arc-type ribbon-helix-helix / Ribbon-helix-helix / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Bifunctional protein PutA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsTanner, J.J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA.
Authors: Zhou, Y. / Larson, J.D. / Bottoms, C.A. / Arturo, E.C. / Henzl, M.T. / Jenkins, J.L. / Nix, J.C. / Becker, D.F. / Tanner, J.J.
History
DepositionSep 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 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 1.3Aug 30, 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 / 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

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*DTP*DT*DTP*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DCP*DAP*DAP*DA)-3')
D: DNA (5'-D(*DTP*DTP*DTP*DGP*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DAP*DAP*DA)-3')
A: Bifunctional protein putA
B: Bifunctional protein putA


Theoretical massNumber of molelcules
Total (without water)25,1904
Polymers25,1904
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.911, 44.084, 55.230
Angle α, β, γ (deg.)90.000, 101.500, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: DNA chain DNA (5'-D(*DTP*DT*DTP*DGP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DCP*DAP*DAP*DA)-3')


Mass: 6404.144 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: the nucleotides 211-231 of the put control region in E. coli
#2: DNA chain DNA (5'-D(*DTP*DTP*DTP*DGP*DAP*DAP*DAP*DGP*DGP*DTP*DGP*DCP*DAP*DAP*DCP*DCP*DGP*DCP*DAP*DAP*DA)-3')


Mass: 6480.224 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: complement strand of the nucleotides 211-231 of the put control region in E. coli
#3: Protein Bifunctional protein putA


Mass: 6152.944 Da / Num. of mol.: 2 / Fragment: Residues 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: putA, poaA / Plasmid: pKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: P09546
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG-MME 550, 50 mM CaCl2, and 100 mM Bis-Tris pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG-MME 55011
2CaCl211
3Bis-Tris11
4PEG-MME 55012
5CaCl212
6Bis-Tris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.24 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 6, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.25→54.153 Å / Num. obs: 10293 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.373.60.4341.6533614880.43499.3
2.37-2.523.60.2922.4509814270.29299.4
2.52-2.693.60.1813.8467512920.18199.5
2.69-2.93.60.1235.6446812470.12399.8
2.9-3.183.60.0749409511420.07499.7
3.18-3.563.60.0539.1372410400.05399.9
3.56-4.113.60.04313.232859210.043100
4.11-5.033.60.04414.328317950.04499.9
5.03-7.123.50.04514.121396070.04599.8
7.12-44.543.30.03616.211033340.03695.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
CNSrefinement
SCALAdata scaling
PDB_EXTRACT3data extraction
Blu-Icedata collection
MOSFLMdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AY0

2ay0


Resolution: 2.25→54.15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.418 / SU ML: 0.144 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.297 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 524 5.1 %RANDOM
Rwork0.206 ---
all0.208 10293 --
obs0.208 10293 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.736 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20.22 Å2
2--0.82 Å20 Å2
3---0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.25→54.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 757 0 27 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211567
X-RAY DIFFRACTIONr_bond_other_d0.0010.021039
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.5512278
X-RAY DIFFRACTIONr_angle_other_deg1.08932465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.638587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.61722.532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65315131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.637158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021157
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02149
X-RAY DIFFRACTIONr_nbd_refined0.1750.2245
X-RAY DIFFRACTIONr_nbd_other0.1880.21059
X-RAY DIFFRACTIONr_nbtor_refined0.2080.2641
X-RAY DIFFRACTIONr_nbtor_other0.0780.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0020.21
X-RAY DIFFRACTIONr_mcbond_it0.6311.5450
X-RAY DIFFRACTIONr_mcbond_other0.1481.5182
X-RAY DIFFRACTIONr_mcangle_it1.1572717
X-RAY DIFFRACTIONr_scbond_it1.40431499
X-RAY DIFFRACTIONr_scangle_it2.0564.51561
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 39 -
Rwork0.218 732 -
all-771 -
obs--98.85 %
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)
13.90111.0471-0.37276.1121-0.37274.00560.0246-0.13810.1986-0.10040.0850.6083-0.0613-0.2071-0.1095-0.1801-0.0228-0.0034-0.2087-0.0037-0.2198-41.204513.02559.7388
23.97090.62381.07185.70521.16955.88940.135-0.4089-0.19190.16870.1619-0.19610.34560.0417-0.2969-0.1086-0.0078-0.0715-0.179-0.008-0.2267-36.11387.558462.2779
320.2148-4.49074.62585.8641-0.85093.8746-0.3635-2.17721.58411.14580.0304-0.0276-0.3068-0.17130.33310.0562-0.07240.1070.1661-0.1997-0.0645-39.815619.720473.4268
426.305615.5344-11.453915.2544-9.695213.1136-1.38010.2748-1.33-1.70930.3156-0.64081.3896-0.73751.06450.0342-0.1020.02-0.03210.02130.1435-11.910118.380365.7519
514.0656-0.77470.50814.2211-0.89732.46910.4091-1.0211.69450.5125-0.3799-0.3887-0.38250.2147-0.0292-0.0343-0.1649-0.03160.1393-0.18010.0094-30.082819.739272.0036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC3 - 465 - 48
2X-RAY DIFFRACTION2BD4 - 486 - 50
3X-RAY DIFFRACTION3CA3 - 143 - 14
4X-RAY DIFFRACTION4CA15 - 2115 - 21
5X-RAY DIFFRACTION5DB1 - 191 - 19

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