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- PDB-7ckv: Crystal structure of Cyanobacteriochrome GAF domain in Pr state -

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Basic information

Entry
Database: PDB / ID: 7ckv
TitleCrystal structure of Cyanobacteriochrome GAF domain in Pr state
ComponentsRcaE
KeywordsSIGNALING PROTEIN / Cyanobacteriochrome
Function / homology
Function and homology information


: / phosphorelay sensor kinase activity
Similarity search - Function
PAS fold-4 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAS domain / PAC domain profile. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / PAC motif ...PAS fold-4 / PAS fold / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS-associated, C-terminal / PAS domain / 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 / 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 / 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
Similarity search - Domain/homology
PHYCOCYANOBILIN / RcaE
Similarity search - Component
Biological speciesMicrochaete diplosiphon (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsNagae, T. / Koizumi, T. / Hirose, Y. / Mishima, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE.
Authors: Nagae, T. / Unno, M. / Koizumi, T. / Miyanoiri, Y. / Fujisawa, T. / Masui, K. / Kamo, T. / Wada, K. / Eki, T. / Ito, Y. / Hirose, Y. / Mishima, M.
History
DepositionJul 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 19, 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 1.2Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RcaE
B: RcaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9845
Polymers40,7822
Non-polymers1,2023
Water6,233346
1
A: RcaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9802
Polymers20,3911
Non-polymers5891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-18 kcal/mol
Surface area7900 Å2
MethodPISA
2
B: RcaE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0043
Polymers20,3911
Non-polymers6132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-20 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.730, 101.334, 41.810
Angle α, β, γ (deg.)90.000, 91.788, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RcaE / Cyanobacteriochrome


Mass: 20391.125 Da / Num. of mol.: 2 / Fragment: GAF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microchaete diplosiphon (bacteria) / Gene: rcaE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q47897
#2: Chemical ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 1.86 Å3/Da / Density % sol: 33.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 27% PEG 4000, 0.2M MgCl2, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 29, 2020
RadiationMonochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.63→41.79 Å / Num. obs: 36876 / % possible obs: 99.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.054 / Χ2: 0.57 / Net I/σ(I): 13.3
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1810 / CC1/2: 0.837 / Rpim(I) all: 0.285 / Rrim(I) all: 0.562 / Χ2: 0.57 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vv4

3vv4


Resolution: 1.63→38.663 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.973 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.089 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1753 4.758 %Random selection
Rwork0.1583 35093 --
all0.16 ---
obs-36846 99.525 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.225 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å2-0 Å2-0.669 Å2
2---0.822 Å2-0 Å2
3----0.275 Å2
Refinement stepCycle: LAST / Resolution: 1.63→38.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 87 346 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132471
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172324
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.6343386
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5685394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6295295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05222.868136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17315417
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg7.966152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4511510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022765
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02465
X-RAY DIFFRACTIONr_nbd_refined0.2240.2459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22205
X-RAY DIFFRACTIONr_nbtor_refined0.170.21127
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21094
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2217
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3240.222
X-RAY DIFFRACTIONr_nbd_other0.180.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.170.222
X-RAY DIFFRACTIONr_mcbond_it1.8931.9041149
X-RAY DIFFRACTIONr_mcbond_other1.8851.91148
X-RAY DIFFRACTIONr_mcangle_it2.7672.8411435
X-RAY DIFFRACTIONr_mcangle_other2.7712.8451436
X-RAY DIFFRACTIONr_scbond_it2.8912.2071322
X-RAY DIFFRACTIONr_scbond_other2.8922.2081321
X-RAY DIFFRACTIONr_scangle_it4.4443.2051943
X-RAY DIFFRACTIONr_scangle_other4.4433.2041944
X-RAY DIFFRACTIONr_lrange_it6.57824.2992749
X-RAY DIFFRACTIONr_lrange_other6.4623.4532658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6720.2271240.2462589X-RAY DIFFRACTION99.8895
1.672-1.7180.2321380.2192504X-RAY DIFFRACTION99.9622
1.718-1.7680.2671170.2032481X-RAY DIFFRACTION99.8847
1.768-1.8220.2181090.1832406X-RAY DIFFRACTION99.9603
1.822-1.8820.2191250.1692334X-RAY DIFFRACTION99.9594
1.882-1.9480.194980.1642222X-RAY DIFFRACTION99.8279
1.948-2.0210.2421210.1632147X-RAY DIFFRACTION99.9559
2.021-2.1040.1981090.1562122X-RAY DIFFRACTION99.9552
2.104-2.1970.222910.1591988X-RAY DIFFRACTION99.7122
2.197-2.3040.221780.1511915X-RAY DIFFRACTION99.6999
2.304-2.4280.178900.1441821X-RAY DIFFRACTION99.5831
2.428-2.5750.212840.1411720X-RAY DIFFRACTION99.6685
2.575-2.7530.215980.1531604X-RAY DIFFRACTION99.5904
2.753-2.9720.207830.1491489X-RAY DIFFRACTION98.7437
2.972-3.2550.182750.161361X-RAY DIFFRACTION98.9662
3.255-3.6370.181660.1441239X-RAY DIFFRACTION99.0888
3.637-4.1960.132610.1281088X-RAY DIFFRACTION98.542
4.196-5.1310.216330.14949X-RAY DIFFRACTION98.2983
5.131-7.2190.17290.178725X-RAY DIFFRACTION97.2903
7.219-38.6630.226240.197389X-RAY DIFFRACTION94.2922

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