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- PDB-6iy8: DmpR-phenol complex of Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 6iy8
TitleDmpR-phenol complex of Pseudomonas putida
ComponentsPositive regulator CapR
KeywordsGENE REGULATION / phenol / transcription / DmpR / CapR / ATPase
Function / homology
Function and homology information


sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Trafficking protein particle complex subunit 3 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. ...Activator of aromatic catabolism / Activator of aromatic catabolism / 4-vinyl reductase, 4VR / V4R domain / V4R / Trafficking protein particle complex subunit 3 / Muramoyl-pentapeptide Carboxypeptidase; domain 2 / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, conserved site / Sigma-54 interaction domain C-terminal part signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / NO signalling/Golgi transport ligand-binding domain superfamily / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / Homeobox-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHENOL / Positive regulator CapR
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsPark, K.H. / Woo, E.J.
Citation
Journal: Nat Commun / Year: 2020
Title: Tetrameric architecture of an active phenol-bound form of the AAA+transcriptional regulator DmpR.
Authors: Park, K.H. / Kim, S. / Lee, S.J. / Cho, J.E. / Patil, V.V. / Dumbrepatil, A.B. / Song, H.N. / Ahn, W.C. / Joo, C. / Lee, S.G. / Shingler, V. / Woo, E.J.
#1: Journal: Structure / Year: 2016
Title: Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator PoxR.
Authors: Patil, V.V. / Park, K.H. / Lee, S.G. / Woo, E.J.
History
DepositionDec 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Positive regulator CapR
B: Positive regulator CapR
C: Positive regulator CapR
D: Positive regulator CapR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,02412
Polymers212,3864
Non-polymers6388
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28540 Å2
ΔGint-99 kcal/mol
Surface area80790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.636, 129.998, 110.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUARGARG(chain 'A' and (resid 16 through 224 or resid 231...AA16 - 2234 - 211
121GLYGLYGLYGLY(chain 'A' and (resid 16 through 224 or resid 231...AA231219
131TYRTYRTYRTYR(chain 'A' and (resid 16 through 224 or resid 231...AA234222
141GLYGLYMETMET(chain 'A' and (resid 16 through 224 or resid 231...AA237 - 249225 - 237
151ALAALAALAALA(chain 'A' and (resid 16 through 224 or resid 231...AA252 - 315240 - 303
161SERSERASPASP(chain 'A' and (resid 16 through 224 or resid 231...AA318 - 361306 - 349
171THRTHRALAALA(chain 'A' and (resid 16 through 224 or resid 231...AA364 - 405352 - 393
181ARGARGARGARG(chain 'A' and (resid 16 through 224 or resid 231...AA409397
191GLUGLUGLYGLY(chain 'A' and (resid 16 through 224 or resid 231...AA411 - 429399 - 417
1101THRTHRILEILE(chain 'A' and (resid 16 through 224 or resid 231...AA432 - 463420 - 451
1111THRTHRARGARG(chain 'A' and (resid 16 through 224 or resid 231...AA466 - 480454 - 468
2121GLUGLUARGARG(chain 'C' and (resid 16 through 224 or resid 231...CC16 - 2234 - 211
2131GLYGLYGLYGLY(chain 'C' and (resid 16 through 224 or resid 231...CC231219
2141TYRTYRTYRTYR(chain 'C' and (resid 16 through 224 or resid 231...CC234222
2151GLYGLYMETMET(chain 'C' and (resid 16 through 224 or resid 231...CC237 - 249225 - 237
2161ALAALAALAALA(chain 'C' and (resid 16 through 224 or resid 231...CC252 - 315240 - 303
2171SERSERASPASP(chain 'C' and (resid 16 through 224 or resid 231...CC318 - 361306 - 349
2181THRTHRALAALA(chain 'C' and (resid 16 through 224 or resid 231...CC364 - 405352 - 393
2191ARGARGARGARG(chain 'C' and (resid 16 through 224 or resid 231...CC409397
2201GLUGLUGLYGLY(chain 'C' and (resid 16 through 224 or resid 231...CC411 - 429399 - 417
2211THRTHRILEILE(chain 'C' and (resid 16 through 224 or resid 231...CC432 - 463420 - 451
2221THRTHRARGARG(chain 'C' and (resid 16 through 224 or resid 231...CC466 - 480454 - 468
1232THRTHRGLUGLU(chain 'B' and (resid 18 through 35 or resid 37...BB18 - 346 - 22
1242METMETARGARG(chain 'B' and (resid 18 through 35 or resid 37...BB37 - 4925 - 37
1252GLUGLULYSLYS(chain 'B' and (resid 18 through 35 or resid 37...BB51 - 6239 - 50
1262PHEPHEARGARG(chain 'B' and (resid 18 through 35 or resid 37...BB65 - 6753 - 55
1272GLYGLYSERSER(chain 'B' and (resid 18 through 35 or resid 37...BB69 - 8857 - 76
1282ASPASPGLYGLY(chain 'B' and (resid 18 through 35 or resid 37...BB91 - 14279 - 130
1292GLNGLNASNASN(chain 'B' and (resid 18 through 35 or resid 37...BB145 - 225133 - 213
1302TYRTYRTYRTYR(chain 'B' and (resid 18 through 35 or resid 37...BB233 - 234221 - 222
1312GLYGLYALAALA(chain 'B' and (resid 18 through 35 or resid 37...BB237 - 241225 - 229
1322THRTHRILEILE(chain 'B' and (resid 18 through 35 or resid 37...BB244 - 272232 - 260
1332SERSERSERSER(chain 'B' and (resid 18 through 35 or resid 37...BB275 - 340263 - 328
1342ALAALATYRTYR(chain 'B' and (resid 18 through 35 or resid 37...BB343 - 428331 - 416
1352THRTHRTHRTHR(chain 'B' and (resid 18 through 35 or resid 37...BB432 - 466420 - 454
1362SERSERPHEPHE(chain 'B' and (resid 18 through 35 or resid 37...BB471 - 478459 - 466
2372THRTHRGLUGLU(chain 'D' and (resid 18 through 35 or resid 37...DD18 - 346 - 22
2382METMETARGARG(chain 'D' and (resid 18 through 35 or resid 37...DD37 - 4925 - 37
2392GLUGLULYSLYS(chain 'D' and (resid 18 through 35 or resid 37...DD51 - 6239 - 50
2402PHEPHEARGARG(chain 'D' and (resid 18 through 35 or resid 37...DD65 - 6753 - 55
2412GLYGLYSERSER(chain 'D' and (resid 18 through 35 or resid 37...DD69 - 8857 - 76
2422ASPASPGLYGLY(chain 'D' and (resid 18 through 35 or resid 37...DD91 - 14279 - 130
2432GLNGLNASNASN(chain 'D' and (resid 18 through 35 or resid 37...DD145 - 225133 - 213
2442TYRTYRTYRTYR(chain 'D' and (resid 18 through 35 or resid 37...DD233 - 234221 - 222
2452GLYGLYALAALA(chain 'D' and (resid 18 through 35 or resid 37...DD237 - 241225 - 229
2462THRTHRILEILE(chain 'D' and (resid 18 through 35 or resid 37...DD244 - 272232 - 260
2472SERSERSERSER(chain 'D' and (resid 18 through 35 or resid 37...DD275 - 340263 - 328
2482ALAALATYRTYR(chain 'D' and (resid 18 through 35 or resid 37...DD343 - 428331 - 416
2492THRTHRTHRTHR(chain 'D' and (resid 18 through 35 or resid 37...DD432 - 466420 - 454
2502SERSERPHEPHE(chain 'D' and (resid 18 through 35 or resid 37...DD471 - 478459 - 466

NCS ensembles :
ID
1
2

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Components

#1: Protein
Positive regulator CapR


Mass: 53096.512 Da / Num. of mol.: 4 / Mutation: C119S, C137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria)
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q7WSM9
#2: Chemical
ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 3.02 Å3/Da / Density % sol: 59.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 340mM Na/K-tartarate, 80mM Glycine, 3mM AMP-PNP, 10mM phenol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.42→30.12 Å / Num. obs: 31309 / % possible obs: 90.5 % / Redundancy: 5.2 % / Biso Wilson estimate: 83.09 Å2 / Rsym value: 0.155 / Net I/σ(I): 8.52
Reflection shellResolution: 3.42→9.15 Å / Rmerge(I) obs: 0.85 / Num. unique obs: 4372

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→30.12 Å / SU ML: 0.4638 / Cross valid method: FREE R-VALUE / σ(F): 1.47 / Phase error: 32.6639
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2856 3117 9.96 %
Rwork0.2328 28189 -
obs0.2382 31306 88.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 103.22 Å2
Refinement stepCycle: LAST / Resolution: 3.42→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14912 0 0 0 14912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002815187
X-RAY DIFFRACTIONf_angle_d0.70120473
X-RAY DIFFRACTIONf_chiral_restr0.04452219
X-RAY DIFFRACTIONf_plane_restr0.00542692
X-RAY DIFFRACTIONf_dihedral_angle_d7.04729219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.470.41061060.3528842X-RAY DIFFRACTION60.11
3.47-3.530.39761040.3217959X-RAY DIFFRACTION67.66
3.53-3.590.34941270.3226974X-RAY DIFFRACTION69.68
3.59-3.660.32991280.27611064X-RAY DIFFRACTION75.4
3.66-3.730.35881200.29431106X-RAY DIFFRACTION77.3
3.73-3.80.32921120.28761185X-RAY DIFFRACTION80.61
3.8-3.890.36931100.27091216X-RAY DIFFRACTION84.3
3.89-3.980.33431250.2681210X-RAY DIFFRACTION85.03
3.98-4.080.31641530.26051285X-RAY DIFFRACTION90.21
4.08-4.180.33171350.25981331X-RAY DIFFRACTION91.68
4.18-4.310.2911420.23351318X-RAY DIFFRACTION93.11
4.31-4.450.24191380.22591385X-RAY DIFFRACTION95.13
4.45-4.60.29441510.21811406X-RAY DIFFRACTION96.29
4.6-4.790.29251570.21691376X-RAY DIFFRACTION96.78
4.79-5.010.26431500.20221431X-RAY DIFFRACTION97.05
5.01-5.270.27841650.21131381X-RAY DIFFRACTION97.29
5.27-5.60.3171650.2431393X-RAY DIFFRACTION97.25
5.6-6.030.3421460.25261431X-RAY DIFFRACTION97.17
6.03-6.630.3041700.24881424X-RAY DIFFRACTION98.21
6.63-7.570.27161460.22521462X-RAY DIFFRACTION98.47
7.57-9.490.22611690.18991496X-RAY DIFFRACTION99.17
9.49-30.120.21661980.18241514X-RAY DIFFRACTION98.67
Refinement TLS params.Method: refined / Origin x: -137.811362882 Å / Origin y: 17.8790464333 Å / Origin z: 27.9443292492 Å
111213212223313233
T0.474297777444 Å20.00696032158039 Å2-0.0329916856065 Å2-0.475922962514 Å20.00842646560629 Å2--0.519857325499 Å2
L0.0513970103805 °20.0427970710133 °20.223716229735 °2-0.0622179268592 °2-0.0125331175325 °2--2.14255076361 °2
S0.0631428788384 Å °0.039456406804 Å °0.053277398876 Å °-0.0534129816642 Å °-0.0513976175774 Å °-0.0375499475167 Å °0.196620671265 Å °-0.0630209366885 Å °-0.031602184788 Å °
Refinement TLS groupSelection details: all

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