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- PDB-5dfy: Structure of the parental state of GAF3 from Slr1393 of Synechocy... -

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Basic information

Entry
Database: PDB / ID: 5dfy
TitleStructure of the parental state of GAF3 from Slr1393 of Synechocystis sp. PCC6803 (in vitro assembled protein/chromophore)
ComponentsHistidine kinase
KeywordsTRANSFERASE / cyanobacteriochrome / phycocyanobilin chromophore / photochromicity / bilin-binding GAF domain / photochrome-related protein
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity
Similarity search - Function
PAS domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...PAS domain / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHYCOCYANOBILIN / histidine kinase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXu, X.-L. / Zhao, K.-H. / Gaertner, W. / Hoeppner, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural elements regulating the photochromicity in a cyanobacteriochrome
Authors: Xu, X.-L. / Hoeppner, A. / Wiebeler, C. / Zhao, K.-H. / Schapiro, I. / Gaertner, W.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 2.0Jan 29, 2020Group: Atomic model / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4452
Polymers24,8571
Non-polymers5891
Water3,945219
1
A: Histidine kinase
hetero molecules

A: Histidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8914
Polymers49,7132
Non-polymers1,1772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3830 Å2
ΔGint-44 kcal/mol
Surface area15990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.940, 62.940, 119.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-993-

HOH

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Components

#1: Protein Histidine kinase /


Mass: 24856.637 Da / Num. of mol.: 1 / Fragment: residues 441-597
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: slr1393 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P73184, histidine kinase
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


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


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.02 M sodium citrate pH 5.6, 0.1 M sodium chloride, 11 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.00894 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00894 Å / Relative weight: 1
ReflectionResolution: 1.6→44.51 Å / Num. obs: 32428 / % possible obs: 99.9 % / Redundancy: 12.71 % / Rsym value: 0.05 / Net I/σ(I): 27.87
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 6.44 / Rsym value: 0.342 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→33.629 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 16.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1806 1612 4.97 %
Rwork0.1546 --
obs0.1559 32422 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1299 0 43 219 1561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091405
X-RAY DIFFRACTIONf_angle_d1.3221918
X-RAY DIFFRACTIONf_dihedral_angle_d15.4508
X-RAY DIFFRACTIONf_chiral_restr0.05194
X-RAY DIFFRACTIONf_plane_restr0.006253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5999-1.6470.22331160.18762503X-RAY DIFFRACTION99
1.647-1.70020.21471250.1832539X-RAY DIFFRACTION100
1.7002-1.76090.21581290.1772502X-RAY DIFFRACTION100
1.7609-1.83140.19381380.16962521X-RAY DIFFRACTION100
1.8314-1.91480.1941450.17292523X-RAY DIFFRACTION100
1.9148-2.01570.20321330.16112551X-RAY DIFFRACTION100
2.0157-2.1420.19451250.15992550X-RAY DIFFRACTION100
2.142-2.30730.18211440.15282542X-RAY DIFFRACTION100
2.3073-2.53940.18081340.15282570X-RAY DIFFRACTION100
2.5394-2.90670.18121410.1652583X-RAY DIFFRACTION100
2.9067-3.66140.19491290.1492646X-RAY DIFFRACTION100
3.6614-33.63610.15081530.14112780X-RAY DIFFRACTION100

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