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- PDB-6ph2: Complete LOV domain from the LOV-HK sensory protein from Brucella... -

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Basic information

Entry
Database: PDB / ID: 6ph2
TitleComplete LOV domain from the LOV-HK sensory protein from Brucella abortus (mutant C69S, construct 15-155)
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
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: 2.34 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 / 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: 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)68,8348
Polymers67,0084
Non-polymers1,8254
Water1,29772
1
A: Blue-light-activated histidine kinase
B: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4174
Polymers33,5042
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-29 kcal/mol
Surface area12510 Å2
MethodPISA
2
C: Blue-light-activated histidine kinase
D: Blue-light-activated histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4174
Polymers33,5042
Non-polymers9132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-29 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.270, 95.860, 107.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA19 - 1406 - 127
21ALAALABB19 - 1406 - 127
12ALAALAAA19 - 1406 - 127
22ALAALACC19 - 1406 - 127
13GLNGLNAA18 - 1405 - 127
23GLNGLNDD18 - 1405 - 127
14ALAALABB19 - 1406 - 127
24ALAALACC19 - 1406 - 127
15ALAALABB19 - 1406 - 127
25ALAALADD19 - 1406 - 127
16ALAALACC19 - 1406 - 127
26ALAALADD19 - 1406 - 127

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 16752.086 Da / Num. of mol.: 4 / Mutation: C69S
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-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.: 72 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: 15% (w/v) PEG 3350 + 0.1 M sodium citrate, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2016 / 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 wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.34→48.63 Å / Num. obs: 29308 / % possible obs: 99.4 % / Redundancy: 7.1 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.154 / Net I/σ(I): 11.6
Reflection shellResolution: 2.34→2.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4523 / CC1/2: 0.506 / Rrim(I) all: 0.624 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T50

3t50


Resolution: 2.34→48.63 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.903 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.26071 1466 5 %RANDOM
Rwork0.22743 ---
obs0.22909 27840 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.838 Å2
Baniso -1Baniso -2Baniso -3
1-2.96 Å20 Å20 Å2
2---0.28 Å2-0 Å2
3----2.68 Å2
Refinement stepCycle: 1 / Resolution: 2.34→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 124 72 4096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0154132
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173647
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.7595639
X-RAY DIFFRACTIONr_angle_other_deg0.4371.7158549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.80419.398166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98715567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3641528
X-RAY DIFFRACTIONr_chiral_restr0.0590.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.093.8951980
X-RAY DIFFRACTIONr_mcbond_other3.0893.8981981
X-RAY DIFFRACTIONr_mcangle_it4.9875.822468
X-RAY DIFFRACTIONr_mcangle_other4.9865.8232469
X-RAY DIFFRACTIONr_scbond_it3.9284.3022152
X-RAY DIFFRACTIONr_scbond_other3.934.3032149
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2966.2353172
X-RAY DIFFRACTIONr_long_range_B_refined8.48145.9044172
X-RAY DIFFRACTIONr_long_range_B_other8.48245.9024171
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A37520.08
12B37520.08
21A37490.07
22C37490.07
31A37950.06
32D37950.06
41B37730.08
42C37730.08
51B37750.07
52D37750.07
61C37300.07
62D37300.07
LS refinement shellResolution: 2.343→2.404 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 100 -
Rwork0.412 1889 -
obs--92.81 %

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