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- PDB-6ph3: LOV-PAS construct from the LOV-HK sensory protein from Brucella a... -

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Basic information

Entry
Database: PDB / ID: 6ph3
TitleLOV-PAS construct from the LOV-HK sensory protein from Brucella abortus (dark-adapted, construct 15-273)
ComponentsBlue-light-activated histidine kinase
KeywordsTRANSFERASE / PAS SUPERFAMILY / BLUE-LIGHT PHOTORECEPTOR / FMN BINDING
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
FLAVIN MONONUCLEOTIDE / Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 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
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
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

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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)123,1128
Polymers121,2864
Non-polymers1,8254
Water1,11762
1
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5564
Polymers60,6432
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-60 kcal/mol
Surface area26100 Å2
MethodPISA
2
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5564
Polymers60,6432
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-61 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.420, 56.930, 114.600
Angle α, β, γ (deg.)90.00, 103.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 30321.566 Da / Num. of mol.: 4
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) / Variant (production host): pLysS / References: UniProt: Q8YC53, histidine kinase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 11, 2016
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: 2.74→47.7 Å / Num. obs: 36012 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 83.44 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.13 / Net I/σ(I): 10.4
Reflection shellResolution: 2.74→2.9 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5428 / CC1/2: 0.874 / Rrim(I) all: 0.91 / % possible all: 93.2

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T50

3t50


Resolution: 2.74→47.7 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.865 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.017 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.871 / SU Rfree Blow DPI: 0.342 / SU Rfree Cruickshank DPI: 0.353
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1801 5 %RANDOM
Rwork0.224 ---
obs0.227 36004 99.2 %-
Displacement parametersBiso mean: 74.45 Å2
Baniso -1Baniso -2Baniso -3
1-16.7351 Å20 Å2-5.1064 Å2
2---32.3827 Å20 Å2
3---15.6476 Å2
Refine analyzeLuzzati coordinate error obs: 0 Å
Refinement stepCycle: 1 / Resolution: 2.74→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8063 0 124 62 8249
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018367HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1811372HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2911SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1296HARMONIC5
X-RAY DIFFRACTIONt_it8367HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion19.59
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1111SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9323SEMIHARMONIC4
LS refinement shellResolution: 2.74→2.82 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.314 134 5 %
Rwork0.293 2545 -
all0.294 2679 -
obs--91.09 %

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