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- PDB-6pps: A blue light illuminated LOV-PAS construct from the LOV-HK sensor... -

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Basic information

Entry
Database: PDB / ID: 6pps
TitleA blue light illuminated LOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (construct 15-273)
ComponentsBlue-light-activated histidine kinase
KeywordsSIGNALING PROTEIN / Brucella abortus / LOV domain / sensor histidine kinases / asymmetric activation
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / ATP binding
Similarity search - Function
Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / PAS fold-3 / PAS fold / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...Signal transduction histidine kinase, HWE region / HWE histidine kinase / HWE histidine kinase / PAS fold-3 / PAS fold / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRinaldi, J. / Fernandez, I. / Shin, H. / Gunawardana, S. / Otero, L.H. / Cerutti, M.L. / Yang, X. / Klinke, S. / Goldbaum, F.A.
Funding support Argentina, 3items
OrganizationGrant numberCountry
National Research Council (NRC, Argentina)2011-2672 Argentina
Other government2014-0959 Argentina
Other government2016-1618 Argentina
CitationJournal: Mbio / Year: 2021
Title: Dimer Asymmetry and Light Activation Mechanism in Brucella Blue-Light Sensor Histidine Kinase.
Authors: Rinaldi, J. / Fernandez, I. / Shin, H. / Sycz, G. / Gunawardana, S. / Kumarapperuma, I. / Paz, J.M. / Otero, L.H. / Cerutti, M.L. / Zorreguieta, A. / Ren, Z. / Klinke, S. / Yang, X. / Goldbaum, F.A.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8828
Polymers127,0574
Non-polymers1,8254
Water1,31573
1
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4414
Polymers63,5292
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-52 kcal/mol
Surface area27460 Å2
MethodPISA
2
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4414
Polymers63,5292
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-57 kcal/mol
Surface area27630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.187, 56.892, 116.054
Angle α, β, γ (deg.)90.000, 103.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Blue-light-activated histidine kinase / BA-LOV-histidine kinase / BA-LOV-HK


Mass: 31764.271 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (strain 2308) (bacteria)
Strain: 2308 / Gene: BAB2_0652 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YKK7, histidine kinase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
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: 2.79 Å3/Da / Density % sol: 55.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 14% (w/v) PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35284 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.056 / Rrim(I) all: 0.128 / Net I/σ(I): 16.85
Reflection shellResolution: 2.8→2.87 Å / Num. unique obs: 3187 / CC1/2: 0.653 / Rpim(I) all: 0.685 / Rrim(I) all: 1.542

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3T50

3t50


Resolution: 2.8→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2542 1995 -
Rwork0.2093 --
obs-34879 99.3 %
Displacement parametersBiso max: 235.11 Å2 / Biso min: 38.42 Å2
Refinement stepCycle: final / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8213 0 124 73 8410
Biso mean--86.77 71.21 -
Num. residues----1027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028526
X-RAY DIFFRACTIONf_angle_d0.53211595
X-RAY DIFFRACTIONf_chiral_restr0.0231303
X-RAY DIFFRACTIONf_plane_restr0.0021481
X-RAY DIFFRACTIONf_dihedral_angle_d12.8473153
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.870.44341350.3732230197
2.87-2.94760.41151420.3422227199
2.9476-3.03430.3571380.32242343100
3.0343-3.13220.33331470.30152339100
3.1322-3.24410.29981310.28292333100
3.2441-3.37390.37211460.26872347100
3.3739-3.52730.33141480.24752351100
3.5273-3.71320.26561380.23182329100
3.7132-3.94560.27151480.21042337100
3.9456-4.24990.24161380.18822353100
4.2499-4.67690.20281440.1652382100
4.6769-5.35210.20681450.16852373100
5.3521-6.73710.23331420.19562380100
6.7371-38.38090.19661480.1654245098
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)
10.1575-0.29971.07930.1985-1.39257.67040.04870.18640.12380.009-0.17310.0518-0.03580.61580.14570.5214-0.00370.09530.6489-0.02520.5415105.2684-3.610117.1046
22.1142-0.723-3.92570.22620.93747.69480.19310.3253-0.02890.0078-0.075-0.00280.0188-0.2677-0.17470.6276-0.1052-0.00490.8769-0.03290.5912106.9312-2.136716.5541
3-0.72510.4172-0.44930.23530.06358.64110.02-0.3275-0.18640.1296-0.2921-0.1693-0.0546-0.00130.29470.77710.0684-0.02451.7926-0.00230.7933143.5059-10.094196.6279
42.43750.766-3.30790.2526-0.81484.67420.044-0.1939-0.19420.0372-0.0722-0.00320.1198-0.01030.00760.50230.0243-0.01570.71820.02180.468140.9114-6.715596.29
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA19 - 300
2X-RAY DIFFRACTION2chain BB17 - 300
3X-RAY DIFFRACTION3chain CC19 - 300
4X-RAY DIFFRACTION4chain DD19 - 300

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