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- PDB-7e90: Crystal structure of the receiver domain (D51E) of the response r... -

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Basic information

Entry
Database: PDB / ID: 7.0E+90
TitleCrystal structure of the receiver domain (D51E) of the response regulator VbrR from Vibrio parahaemolyticus
ComponentsDNA-binding response regulator
KeywordsTRANSCRIPTION / transcriptional regulation / receiver domain / response regulator / VbrR / Vibrio parahaemolyticus
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
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 response regulator
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCho, S.Y. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Structural analysis of the activation and DNA interactions of the response regulator VbrR from Vibrio parahaemolyticus.
Authors: Cho, S.Y. / Yoon, S.I.
History
DepositionMar 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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_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: DNA-binding response regulator
B: DNA-binding response regulator


Theoretical massNumber of molelcules
Total (without water)27,9522
Polymers27,9522
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.128, 74.128, 108.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSPROPRO(chain 'A' and ((resid 2 and (name N or name...AA2 - 648 - 70
12TRPTRPARGARG(chain 'A' and ((resid 2 and (name N or name...AA66 - 11672 - 122
23LYSLYSPROPRO(chain 'B' and (resid 2 through 27 or (resid 28...BB2 - 648 - 70
24TRPTRPARGARG(chain 'B' and (resid 2 through 27 or (resid 28...BB66 - 11672 - 122

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Components

#1: Protein DNA-binding response regulator


Mass: 13976.006 Da / Num. of mol.: 2 / Fragment: receiver domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Gene: C1S91_03975 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R9VV79
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 400, Tris, lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 14862 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.4
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.546 / Num. unique obs: 708 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZWM

2zwm


Resolution: 2.25→30 Å / SU ML: 0.211 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.273 722 4.89 %
Rwork0.233 14056 -
obs0.2346 14056 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 0 34 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411814
X-RAY DIFFRACTIONf_angle_d0.8042471
X-RAY DIFFRACTIONf_chiral_restr0.0516299
X-RAY DIFFRACTIONf_plane_restr0.0053318
X-RAY DIFFRACTIONf_dihedral_angle_d20.3191109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.430.25991470.25542697X-RAY DIFFRACTION98.58
2.43-2.670.29661460.27332759X-RAY DIFFRACTION99.42
2.67-3.060.28781230.26522803X-RAY DIFFRACTION99.63
3.06-3.850.3081250.22792849X-RAY DIFFRACTION99.66
3.85-300.25291810.21232948X-RAY DIFFRACTION99.4
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)
14.07834324049-0.331723965521-0.9630880225263.447547237111.104858953655.23531885846-0.1554056916080.5155659657780.0788398389477-0.133601489971-0.1201989986150.1816637997790.0451788970316-0.3051587546140.2288325325020.346960192643-0.00908947286104-0.01500143143980.3557023298160.03167896513020.248675065707-15.2304985253-25.18245051149.10054858021
27.10288605650.908714406114-1.007577177912.67963346834-1.477708156054.53722969351-0.341940797430.9405121287721.11353371183-0.6948866406670.01578979492460.171551023693-0.667495710832-0.01499897868510.1494181749110.5299500561760.00107058747808-0.1274279456390.3232899202570.09051161633620.483751538522-11.3666345442-14.381523486110.4373118643
32.68245226529-0.388087850413-2.130995573322.6115011607-0.2694921966297.142140530780.3343298362430.07540644340320.740578998892-0.437424910292-0.21115483260.0328385401111-1.195626839570.6317114981-0.08357508886420.611843723309-0.166752061073-0.01740360705630.4789362889750.0298518261290.40880270898-5.69811685967-14.663355224216.7496068535
44.141870362330.6904914697961.140557655792.89216423481.225342017965.95853072821-0.2100192006830.07910071346970.242822919918-0.004453088845010.01760012717740.134069331787-0.323045529040.06363788905670.1804660000720.2895208137160.008975713542130.03708584682370.1949314578870.0228471781170.189285762424-8.86913084422-24.350768705423.2299601862
54.04712927236-0.197605063404-0.8283374184351.10999690646-0.9960887096294.94764443902-0.233452441394-0.2549886135180.05715416905260.1506293808810.145932904098-0.4305376344830.352880422107-0.0366374054650.1005188693050.3378632415210.0629053533461-0.01020702395560.339312123752-0.1053761010630.250640955632-8.43006397952-22.208589198346.9902567046
65.863786062493.29937443294-2.336039627825.3296562908-1.614616800837.191253949540.727523646552-0.6153498047270.9504523146180.638076065983-0.007416143459230.632985255389-1.00851046723-0.196952857252-0.4175857928170.4892447083620.01371412285450.09648893821130.39480113617-0.1750387532190.392737312895-11.6583753905-17.067790470247.1674129526
77.746205847542.96005910846-1.283495762795.36812874668-0.6695025251356.90274033058-0.20498065586-0.6948874078850.6003655810380.8101352067230.0929031044614-0.08893528210030.361679231401-1.64875447174-0.1122722292450.518877044082-0.04660176255530.0391471410760.652799058249-0.0677514993380.323756061426-22.4496505551-23.413238447947.9528945708
83.282533781630.05961748339580.1817816973623.471534706310.8655992011475.30724643108-0.0436112543124-0.36781768626-0.1700940182410.510250121234-0.0853932283031-0.05704969244770.903418575031-0.4106043260160.1896750826910.428240507481-0.0541721709479-0.01255957357190.460086946247-0.0494255446290.241608058804-17.2410436449-28.790592184542.1222084213
95.34420153328-0.9199150912010.9397194130817.170965326670.6452880998537.404680393820.340218966132-0.504539422659-0.9022679529671.22875497309-0.525050498920.9066576459740.494301787781-1.749294569250.2900609678960.345389024663-0.150643927940.02354324229640.823122116011-0.09322641262860.502748495317-26.233759098-27.339783685438.9534770576
103.345873636480.6185653906680.864650960914.138402515471.216707295225.24725277206-0.3447903969520.219498483569-0.3988867872180.1722006159830.1913108248840.1820552627950.549405096012-0.6748491912170.1439857033910.407932589176-0.03124504693970.0166506380920.3558988962947.12685519587E-50.235046032001-14.6259799997-28.912527516133.3869827142
112.27514686953-0.2206075624531.463955004915.245735873841.064676910658.29938965618-0.008598006479050.008058029999931.11270245588-0.207402238539-0.231659353280.256169770817-0.628994948847-0.1710344597980.104316105980.5180917814770.05841449154060.0406101232660.2485985201050.02016019496080.399994546037-7.50665504537-17.893102396734.1614766488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 78 )
4X-RAY DIFFRACTION4chain 'A' and (resid 79 through 116 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 24 )
6X-RAY DIFFRACTION6chain 'B' and (resid 25 through 32 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 44 )
8X-RAY DIFFRACTION8chain 'B' and (resid 45 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 69 )
10X-RAY DIFFRACTION10chain 'B' and (resid 70 through 103 )
11X-RAY DIFFRACTION11chain 'B' and (resid 104 through 116 )

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