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- PDB-5epv: Histidine kinase domain from the LOV-HK blue-light receptor from ... -

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Basic information

Entry
Database: PDB / ID: 5epv
TitleHistidine kinase domain from the LOV-HK blue-light receptor from Brucella abortus
ComponentsBlue-light-activated histidine kinase
KeywordsTRANSFERASE / Histidine kinase / HWE family / S-SAD phasing / multi-crystal data collection
Function / homology
Function and homology information


protein histidine kinase activity / response to stimulus / 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 / Blue-light-activated histidine kinase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.51 Å
AuthorsRinaldi, J. / Guimaraes, B.G. / Legrand, P. / Thompson, A. / Paris, G. / Goldbaum, F.A. / Klinke, S.
Funding support Argentina, 2items
OrganizationGrant numberCountry
Agencia Nacional de Promocion Cientifica y TecnologicaPICT 2011-2672 Argentina
National Scientific and Technical Research Council (CONICET)PIP 2012-2014 GI 220110100970 Argentina
Citation
Journal: J.Mol.Biol. / Year: 2016
Title: Structural Insights into the HWE Histidine Kinase Family: The Brucella Blue Light-Activated Histidine Kinase Domain.
Authors: Rinaldi, J. / Arrar, M. / Sycz, G. / Cerutti, M.L. / Berguer, P.M. / Paris, G. / Estrin, D.A. / Marti, M.A. / Klinke, S. / Goldbaum, F.A.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of ...Title: S-SAD phasing of monoclinic histidine kinase from Brucella abortus combining data from multiple crystals and orientations: an example of data-collection strategy and a posteriori analysis of different data combinations.
Authors: Klinke, S. / Foos, N. / Rinaldi, J.J. / Paris, G. / Goldbaum, F.A. / Legrand, P. / Guimaraes, B.G. / Thompson, A.
History
DepositionNov 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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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)106,48910
Polymers104,4204
Non-polymers2,0696
Water00
1
C: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6102
Polymers26,1051
Non-polymers5051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6102
Polymers26,1051
Non-polymers5051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2696
Polymers52,2102
Non-polymers1,0594
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-47 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.390, 100.840, 71.410
Angle α, β, γ (deg.)90.00, 102.75, 90.00
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: 26104.926 Da / Num. of mol.: 4 / Fragment: HK domain (UNP residues 266-489)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: BAB2_0652 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2YKK7, histidine kinase
#2: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.2 % / Description: Long bars
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 7.5% w/v PEG8000, 0.1 M HEPES, pH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011,1.80000
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012 / Details: Kirkpatrick-Baez pair of bimorph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.980111
21.81
ReflectionResolution: 2.51→50 Å / Num. all: 32760 / Num. obs: 32760 / % possible obs: 97.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 72 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 2.51→2.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 2 / % possible all: 95.1

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata scaling
PHASERphasing
SHELXphasing
MOLREPphasing
BUSTER2.10.0refinement
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.51→48.55 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.355 / SU Rfree Blow DPI: 0.245 / SU Rfree Cruickshank DPI: 0.255
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 1644 5.02 %RANDOM
Rwork0.2019 ---
obs0.2039 32719 98.13 %-
Displacement parametersBiso mean: 74.01 Å2
Baniso -1Baniso -2Baniso -3
1--13.0427 Å20 Å24.3065 Å2
2---3.2541 Å20 Å2
3---16.2968 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.51→48.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 126 0 5740
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015862HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.218001HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1946SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes121HARMONIC2
X-RAY DIFFRACTIONt_gen_planes917HARMONIC5
X-RAY DIFFRACTIONt_it5862HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion22.64
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion796SEMIHARMONIC5
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_contact6582SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.59 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2608 162 5.48 %
Rwork0.2326 2794 -
all0.2342 2956 -
obs--98.13 %

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