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- PDB-6ph4: Full length LOV-PAS-HK construct from the LOV-HK sensory protein ... -

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Basic information

Entry
Database: PDB / ID: 6ph4
TitleFull length LOV-PAS-HK construct from the LOV-HK sensory protein from Brucella abortus (light-adapted, construct 15-489)
ComponentsBlue-light-activated histidine kinase
KeywordsTRANSFERASE / PAS SUPERFAMILY / BLUE-LIGHT PHOTORECEPTOR / FMN BINDING / HISTIDINE KINASE
Function / homology
Function and homology information


protein histidine kinase activity / histidine kinase / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / FLAVIN MONONUCLEOTIDE / Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsRinaldi, J. / Otero, L.H. / Fernandez, I. / Goldbaum, F.A. / Shin, H. / Yang, X. / Klinke, S.
Funding support Argentina, 3items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2011-2672 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2014-0959 Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT 2016-1618 Argentina
Citation
Journal: 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.
#1: Journal: Biochem Biophys Rep / Year: 2018
Title: Crystallization and initial X-ray diffraction analysis of the multi-domain Brucella blue light-activated histidine kinase LOV-HK in its illuminated state
Authors: Rinaldi, J. / Fernandez, I. / Poth, L.M. / Shepard, W.E. / Savko, M. / Goldbaum, F.A. / Klinke, S.
History
DepositionJun 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2139
Polymers108,6642
Non-polymers1,5497
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10250 Å2
ΔGint-110 kcal/mol
Surface area41680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.956, 104.662, 164.828
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 54332.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094) (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0679 / Plasmid: pET-24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q8YC53, histidine kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 15% (v/v) MPD + 4% (w/v) PEG 4000 + 0.1 M Hepes, pH 7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 26, 2017
Details: CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS
RadiationMonochromator: CRYOGENICALLY COOLED CHANNEL CUT SI[111] CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.25→62.53 Å / Num. obs: 26861 / % possible obs: 100 % / Redundancy: 14.8 % / Biso Wilson estimate: 92 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.118 / Net I/σ(I): 13.1
Reflection shellResolution: 3.25→3.47 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4778 / CC1/2: 0.609 / Rrim(I) all: 2.774 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T50 and 5EPV

3t50

5epv


Resolution: 3.25→62.52 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 0.47 / Phase error: 38.45
RfactorNum. reflection% reflection
Rfree0.3178 2541 5.04 %
Rwork0.2549 --
obs0.2581 26791 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→62.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6144 0 97 0 6241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036370
X-RAY DIFFRACTIONf_angle_d0.6868649
X-RAY DIFFRACTIONf_dihedral_angle_d6.2783828
X-RAY DIFFRACTIONf_chiral_restr0.044969
X-RAY DIFFRACTIONf_plane_restr0.0051109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.31250.46881320.41332667X-RAY DIFFRACTION100
3.3125-3.38010.45791700.41032655X-RAY DIFFRACTION100
3.3801-3.45360.46941320.40112641X-RAY DIFFRACTION100
3.4536-3.53390.36871440.3742654X-RAY DIFFRACTION100
3.5339-3.62230.42331330.34742665X-RAY DIFFRACTION100
3.6223-3.72020.37291270.3272676X-RAY DIFFRACTION100
3.7202-3.82970.41791540.32262673X-RAY DIFFRACTION100
3.8297-3.95330.32481470.30442669X-RAY DIFFRACTION100
3.9533-4.09460.35881310.29222633X-RAY DIFFRACTION100
4.0946-4.25850.36481360.28332679X-RAY DIFFRACTION100
4.2585-4.45220.29571310.27252678X-RAY DIFFRACTION100
4.4522-4.68690.33091440.24562637X-RAY DIFFRACTION100
4.6869-4.98040.26481450.23292678X-RAY DIFFRACTION100
4.9804-5.36480.32151280.23742664X-RAY DIFFRACTION100
5.3648-5.90430.35811520.27812674X-RAY DIFFRACTION100
5.9043-6.75780.30451370.27152652X-RAY DIFFRACTION100
6.7578-8.51070.27181500.23092647X-RAY DIFFRACTION100
8.5107-62.53140.27671480.18562651X-RAY DIFFRACTION100

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