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- PDB-6uvb: Crystal structure of far-red-light absorbing cyanobacteriochrome ... -

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Basic information

Entry
Database: PDB / ID: 6uvb
TitleCrystal structure of far-red-light absorbing cyanobacteriochrome at 100K
ComponentsMulti-sensor signal transduction histidine kinase
KeywordsSIGNALING PROTEIN / Photoreceptor / bilin-binding protein / far-red light
Function / homology
Function and homology information


phosphorelay sensor kinase activity
Similarity search - Function
PAS fold-3 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...PAS fold-3 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / CBS domain / CBS domain / CBS domain profile. / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS domain / PAS repeat profile. / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Multi-sensor signal transduction histidine kinase
Similarity search - Component
Biological speciesAnabaena cylindrica
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYang, X. / Ren, Z. / Bandara, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY024363 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Crystal structure of a far-red-sensing cyanobacteriochrome reveals an atypical bilin conformation and spectral tuning mechanism.
Authors: Bandara, S. / Rockwell, N.C. / Zeng, X. / Ren, Z. / Wang, C. / Shin, H. / Martin, S.S. / Moreno, M.V. / Lagarias, J.C. / Yang, X.
History
DepositionNov 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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: Multi-sensor signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6452
Polymers22,0561
Non-polymers5891
Water724
1
A: Multi-sensor signal transduction histidine kinase
hetero molecules

A: Multi-sensor signal transduction histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2894
Polymers44,1122
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/21
Buried area5120 Å2
ΔGint-54 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.788, 108.788, 68.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222

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Components

#1: Protein Multi-sensor signal transduction histidine kinase


Mass: 22056.049 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena cylindrica (strain ATCC 27899 / PCC 7122) (bacteria)
Strain: ATCC 27899 / PCC 7122 / Gene: Anacy_2551 / Production host: Escherichia coli (E. coli) / References: UniProt: K9ZI18
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 4.61 Å3/Da / Density % sol: 73.31 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: The protein solution (3 mg/ml) is mixed with the crystallization solution (17% PEG 10000, 0.1 M ammonium acetate, 0.1 M Bis-tris pH 5.5 with Yttrium(III) chloride as an additive) in a 1:1 ratio

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9787 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 9394 / % possible obs: 98.9 % / Redundancy: 6.7 % / Biso Wilson estimate: 98.98 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.087 / Χ2: 1.235 / Net I/σ(I): 10.4 / Num. measured all: 63276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.956.51.6884560.4880.7051.8340.556100
2.95-36.91.4824680.7090.61.6020.569100
3-3.066.91.2154600.7340.4941.3140.592100
3.06-3.126.90.9794700.8020.3961.0580.644100
3.12-3.1970.7844490.8060.3190.8490.592100
3.19-3.2770.5544760.9220.2240.5990.646100
3.27-3.356.70.4374590.9440.1830.4760.672100
3.35-3.446.20.3224540.9510.140.3520.81699.8
3.44-3.545.90.2484270.9520.110.2730.86891
3.54-3.656.70.1874730.9830.0780.2030.99998.3
3.65-3.787.40.1924620.9860.0750.2071.175100
3.78-3.947.40.1584600.9920.0620.171.169100
3.94-4.117.30.124720.9920.0470.1291.305100
4.11-4.337.10.0964810.9950.0390.1041.715100
4.33-4.66.90.0674760.9970.0280.0732.09399.8
4.6-4.966.90.0514780.9980.0210.0551.722100
4.96-5.466.80.0494840.9980.020.0531.707100
5.46-6.246.10.0534870.9970.0230.0581.926100
6.24-7.865.90.044660.9990.0170.0442.32692.6
7.86-506.30.0395360.9980.0160.0422.52597.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GLQ

4glq


Resolution: 3→39.703 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2897 410 4.77 %
Rwork0.2365 8189 -
obs0.2389 8599 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 317.63 Å2 / Biso mean: 152.085 Å2 / Biso min: 63.53 Å2
Refinement stepCycle: final / Resolution: 3→39.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1503 0 43 4 1550
Biso mean--133.35 109.57 -
Num. residues----183
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121578
X-RAY DIFFRACTIONf_angle_d1.4932147
X-RAY DIFFRACTIONf_chiral_restr0.06238
X-RAY DIFFRACTIONf_plane_restr0.006271
X-RAY DIFFRACTIONf_dihedral_angle_d23.529933
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.10730.3381400.3705806100
3.1073-3.23170.2978390.3059792100
3.2317-3.37870.347490.2829812100
3.3787-3.55670.3371310.339176995
3.5567-3.77940.325450.284280999
3.7794-4.07090.4563360.2941822100
4.0709-4.48010.3481420.2423820100
4.4801-5.12720.2335380.1984838100
5.1272-6.45520.239490.2385849100
6.4552-39.7030.2518410.181187295
Refinement TLS params.Method: refined / Origin x: 20.586 Å / Origin y: 46.158 Å / Origin z: 20.0684 Å
111213212223313233
T0.9487 Å20.5958 Å20.2503 Å2-1.5565 Å20.2045 Å2--0.6364 Å2
L16.2429 °2-6.2559 °25.0248 °2-6.1754 °21.1519 °2--5.443 °2
S-1.5483 Å °-2.3993 Å °-1.3054 Å °1.4403 Å °1.4488 Å °0.5055 Å °0.1988 Å °-0.1882 Å °0.0717 Å °
Refinement TLS groupSelection details: chain A

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