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- PDB-6lxm: Crystal structure of C-terminal DNA-binding domain of Escherichia... -

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Basic information

Entry
Database: PDB / ID: 6lxm
TitleCrystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR as a domain-swapped dimer
ComponentsTranscriptional regulatory protein OmpR
KeywordsDNA BINDING PROTEIN / DNA binding protein Transcription factor / TRANSCRIPTION
Function / homology
Function and homology information


phosphorelay response regulator activity / phosphorelay signal transduction system / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA-binding dual transcriptional regulator OmpR / DNA-binding dual transcriptional regulator OmpR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.412 Å
AuthorsSadotra, S. / Chen, C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)108-2113-M-002-011 Taiwan
Ministry of Science and Technology (MoST, Taiwan)108-2628-B-002-013 Taiwan
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structural basis for promoter DNA recognition by the response regulator OmpR.
Authors: Sadotra, S. / Lou, Y.C. / Tang, H.C. / Chiu, Y.C. / Hsu, C.H. / Chen, C.
History
DepositionFeb 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Transcriptional regulatory protein OmpR
A: Transcriptional regulatory protein OmpR
B: Transcriptional regulatory protein OmpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,91219
Polymers39,2973
Non-polymers1,61416
Water2,216123
1
C: Transcriptional regulatory protein OmpR
hetero molecules

C: Transcriptional regulatory protein OmpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,17710
Polymers26,1982
Non-polymers9798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
2
A: Transcriptional regulatory protein OmpR
B: Transcriptional regulatory protein OmpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,32314
Polymers26,1982
Non-polymers1,12512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.683, 98.683, 92.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-58-

ARG

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Components

#1: Protein Transcriptional regulatory protein OmpR


Mass: 13099.091 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ompR, NCTC10764_03768 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A376JR14, UniProt: P0AA16*PLUS
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Potassium phosphate monobasic/sodium phosphate diabasic pH6.2 2.5M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.41→26.45 Å / Num. obs: 19976 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.974 / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.1
Reflection shellResolution: 2.41→2.49 Å / Num. unique obs: 19976 / CC1/2: 0.893

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: solved structure

Resolution: 2.412→26.45 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.62
RfactorNum. reflection% reflection
Rfree0.2213 1982 9.92 %
Rwork0.1817 --
obs0.1857 19976 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.66 Å2 / Biso mean: 45.0144 Å2 / Biso min: 17.72 Å2
Refinement stepCycle: final / Resolution: 2.412→26.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 98 123 2659
Biso mean--89.77 45.18 -
Num. residues----302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.412-2.47210.26311130.2068106082
2.4721-2.53890.26421320.2116119093
2.5389-2.61350.27671400.2217127098
2.6135-2.69780.31631450.2231299100
2.6978-2.79410.26721430.22821287100
2.7941-2.90590.31381410.20921304100
2.9059-3.0380.23871430.19471291100
3.038-3.19790.25361480.20511300100
3.1979-3.39790.2121410.19131311100
3.3979-3.65970.21411440.17181307100
3.6597-4.02690.17871410.15021312100
4.0269-4.60720.17641520.14351323100
4.6072-5.79530.20751440.16391348100
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)
10.89660.46030.96881.63260.20191.58060.2715-0.2086-0.17830.9375-0.0181-0.61960.1564-0.0787-0.08780.56520.0378-0.16740.2514-0.00450.31925.036834.503524.3428
22.2527-0.1760.51324.11751.53734.223-0.18780.2154-0.009-0.36750.34610.2094-0.21780.3089-0.15680.37090.0062-0.00790.2118-0.01340.378125.878142.51459.7446
31.59520.7735-0.62271.2855-0.72972.0812-0.07770.2963-0.163-0.13920.1352-0.05960.2809-0.0941-0.0660.2716-0.0403-0.01190.29390.02940.355428.993337.3799-15.9107
44.4715-0.7760.33743.876-0.36832.61570.12860.3332-0.51830.21160.32840.0782-0.0434-0.513-0.41890.3355-0.0156-0.05680.39850.00170.32862.373125.4078-21.4763
52.17480.417-1.13612.06640.32823.0257-0.0808-0.1978-0.3397-0.05220.01950.18640.17810.1909-0.04810.23570.026-0.05550.28160.09330.3025-0.246328.8372-11.2352
61.56840.2314-0.04521.5759-0.47942.0338-0.00730.05270.0079-0.1127-0.1981-0.11620.20530.33950.21370.2442-0.00430.00520.42820.13180.2767.559622.093112.6272
72.79340.00310.80862.9683-0.07342.9545-0.1445-0.3078-0.51410.2941-0.0937-0.10160.18150.00210.21930.3248-0.08620.07150.42150.09310.3-2.765415.05719.9149
81.39890.63380.29870.52650.45020.96530.1487-1.06910.15270.7558-0.35650.2916-0.79110.320.14540.6161-0.21140.09820.6925-0.01210.30894.009326.988428.3273
91.24632.0394-0.13243.6497-1.48933.8157-0.34730.66350.51970.12780.40770.1730.096-0.1876-0.02960.3067-0.00580.03830.41390.06650.3468-2.763427.35112.9119
102.54210.17420.11372.1066-1.03836.70480.1262-0.15240.15710.0805-0.3521-0.1673-0.6690.70540.17370.2531-0.0249-0.01830.33110.04360.36743.168438.1112-5.4557
112.3299-0.6105-0.18982.33290.36852.4542-0.06410.28120.0439-0.1502-0.10760.1432-0.1846-0.05240.11360.17110.0321-0.03680.31740.06530.3075-7.757337.8491-16.2319
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 2 through 41 )C2 - 41
2X-RAY DIFFRACTION2chain 'C' and (resid 42 through 56 )C42 - 56
3X-RAY DIFFRACTION3chain 'C' and (resid 57 through 102 )C57 - 102
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 20 )A2 - 20
5X-RAY DIFFRACTION5chain 'A' and (resid 21 through 57 )A21 - 57
6X-RAY DIFFRACTION6chain 'A' and (resid 58 through 78 )A58 - 78
7X-RAY DIFFRACTION7chain 'A' and (resid 79 through 101 )A79 - 101
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 41 )B2 - 41
9X-RAY DIFFRACTION9chain 'B' and (resid 42 through 56 )B42 - 56
10X-RAY DIFFRACTION10chain 'B' and (resid 57 through 78 )B57 - 78
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 102 )B79 - 102

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