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- PDB-5nwn: Deinococcus radiodurans BphP PAS-GAF-PHY Y263F mutant, dark -

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Basic information

Entry
Database: PDB / ID: 5nwn
TitleDeinococcus radiodurans BphP PAS-GAF-PHY Y263F mutant, dark
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Kinase / Photosensor / Phytochrome
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
PHY domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily ...PHY domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / PAS domain / 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 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.6 Å
AuthorsTakala, H. / Westehoff, S. / Ihalainen, J.A.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome.
Authors: Takala, H. / Lehtivuori, H.K. / Berntsson, O. / Hughes, A. / Nanekar, R. / Niebling, S. / Panman, M. / Henry, L. / Menzel, A. / Westenhoff, S. / Ihalainen, J.A.
History
DepositionMay 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,6038
Polymers226,2604
Non-polymers2,3434
Water0
1
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3014
Polymers113,1302
Non-polymers1,1712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3014
Polymers113,1302
Non-polymers1,1712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.110, 197.120, 214.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12B
22A
32C
42D
13C
23A
33B
43D
14D
24A
34B
44C

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LBV / End label comp-ID: LBV / Refine code: 1 / Auth seq-ID: 7 - 600 / Label seq-ID: 21

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA - E
21BB - F
31CC - G
41DD - H
12BB - F
22AA - E
32CC - G
42DD - H
13CC - G
23AA - E
33BB - F
43DD - H
14DD - H
24AA - E
34BB - F
44CC - G

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.975792, -0.218699, 0.001178), (-0.218658, 0.975689, 0.014791), (-0.004384, 0.014176, -0.99989)85.545486, 9.57666, -10.18035
3given(-0.240456, 0.97, 0.035781), (0.97066, 0.240267, 0.009537), (0.000654, 0.037025, -0.999314)-161.951187, 127.580994, -69.099243
4given(-0.027155, -0.999204, -0.029217), (0.998641, -0.025816, -0.045264), (0.044474, -0.030406, 0.998548)218.924164, 176.43602, 57.71624
5given(1), (1), (1)
6given(-0.975792, -0.218658, -0.004384), (-0.218699, 0.975689, 0.014176), (0.001178, 0.014791, -0.99989)85.523956, 9.50915, -10.42167
7given(0.022389, -0.999217, -0.032619), (0.999659, 0.022813, -0.012686), (0.013421, -0.032324, 0.999387)215.960953, 168.427551, 60.366249
8given(-0.192059, 0.980793, 0.034029), (0.980933, 0.192905, -0.023619), (-0.029729, 0.028844, -0.999142)-166.932617, 134.595657, -65.263893
9given(1), (1), (1)
10given(-0.240456, 0.97066, 0.000654), (0.97, 0.240267, 0.037025), (0.035781, 0.009537, -0.999314)-162.734665, 128.997528, -64.47374
11given(0.022389, 0.999659, 0.013421), (-0.999217, 0.022813, -0.032324), (-0.032619, -0.012686, 0.999387)-174.015549, 213.900711, -51.148109
12given(0.9759, 0.215186, -0.036258), (0.215248, -0.976557, -0.002245), (-0.035891, -0.005613, -0.99934)-44.079151, 385.882812, -112.634392
13given(1), (1), (1)
14given(-0.027155, 0.998641, 0.044474), (-0.999204, -0.025816, -0.030406), (-0.029217, -0.045264, 0.998548)-172.818359, 225.059723, -43.249931
15given(-0.192059, 0.980933, -0.029729), (0.980793, 0.192905, 0.028844), (0.034029, -0.023619, -0.999142)-166.030426, 139.644638, -56.348351
16given(0.9759, 0.215248, -0.035891), (0.215186, -0.976557, -0.005613), (-0.036258, -0.002245, -0.99934)-44.086079, 385.689484, -113.291893

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Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56565.027 Da / Num. of mol.: 4 / Mutation: Y263F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Gene: bphP, DR_A0050 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical
ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H37N4O6

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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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris/HCL pH 8.5, 200 mM sodium acetate trihydrate, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97779 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 30, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 3.6→19.94 Å / Num. obs: 40750 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4.389 % / Biso Wilson estimate: 139.832 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.082 / Χ2: 1.008 / Net I/σ(I): 11.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.6-3.694.5221.4140.929470.3431.59298.8
3.69-3.84.5131.121.231500.4591.26298
3.8-44.3550.6582.0449310.6970.74797.4
4-84.4030.09712.27261150.9950.11197.4
8-154.1650.02737.4732520.9990.03195.1
15-19.943.6280.02737.753550.9990.03150.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.83 Å19.94 Å
Translation7.83 Å19.94 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALENov 1, 2016data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C5K

5c5k


Resolution: 3.6→19.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 46.295 / SU ML: 0.638 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.653
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 2037 5 %RANDOM
Rwork0.2475 ---
obs0.2495 38682 96.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 339.54 Å2 / Biso mean: 195.18 Å2 / Biso min: 87.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.1 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 3.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14443 0 172 0 14615
Biso mean--190.11 --
Num. residues----1891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915005
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214332
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.98820527
X-RAY DIFFRACTIONr_angle_other_deg0.88332885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39151875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47523.185631
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.641152223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.35915119
X-RAY DIFFRACTIONr_chiral_restr0.0590.22311
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116935
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023328
Refine LS restraints NCS

Number: 7162 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDRms dev position (Å)
11A44.44
12B38.22
13C42.9
14D40.09
21B38.22
22A44.44
23C42.9
24D40.09
31C42.9
32A44.44
33B38.22
34D40.09
41D40.09
42A44.44
43B38.22
44C42.9
LS refinement shellResolution: 3.6→3.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 145 -
Rwork0.373 2783 -
all-2928 -
obs--98.75 %

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