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- PDB-5nm3: Deinococcus radiodurans BphP PAS-GAF-PHY Y263F mutant, pre-illuminated -

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Basic information

Entry
Database: PDB / ID: 5nm3
TitleDeinococcus radiodurans BphP PAS-GAF-PHY Y263F mutant, pre-illuminated
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: 3.3 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
DepositionApr 5, 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 / _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: Bacteriophytochrome
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,6038
Polymers226,2604
Non-polymers2,3434
Water905
1
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3014
Polymers113,1302
Non-polymers1,1712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-37 kcal/mol
Surface area40450 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3014
Polymers113,1302
Non-polymers1,1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-38 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.700, 198.500, 223.600
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 7 - 502 / Label seq-ID: 21 - 516

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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: 4.2 Å3/Da / Density % sol: 70.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM Tris/HCl pH 8.5, 200 mM NaCl, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.3→19.98 Å / Num. obs: 57827 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.094 % / Biso Wilson estimate: 81.738 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.18 / Χ2: 0.931 / Net I/σ(I): 7.68 / Num. measured all: 236771 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.3-3.384.3091.4690.9640960.3121.67799.9
3.38-3.54.2791.0671.3451690.4941.2299.7
3.5-3.64.2740.7951.8339030.6120.9199.7
3.6-3.74.2230.6822.1134750.6810.78199.7
3.7-44.1580.4343.2185250.840.49899.8
4-84.0060.1259.75286310.9840.14499.6
8-153.8450.03627.4336280.9980.04199.2
15-19.983.9020.02932.534000.9990.03354.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.96 Å19.98 Å
Translation7.96 Å19.98 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: 3.3→19.98 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.913 / SU B: 32.302 / SU ML: 0.475 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.472
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2668 2890 5 %RANDOM
Rwork0.2335 ---
obs0.2351 54898 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 221.28 Å2 / Biso mean: 114.215 Å2 / Biso min: 48.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 3.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14790 0 344 5 15139
Biso mean--100.31 80.35 -
Num. residues----1937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01915555
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214778
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.99821295
X-RAY DIFFRACTIONr_angle_other_deg0.922333886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78451921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08823.225648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.299152264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.11815120
X-RAY DIFFRACTIONr_chiral_restr0.0630.22362
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117520
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023428
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A581960.03
12B581960.03
21A580460.02
22C580460.02
31A576200.03
32D576200.03
41B577860.03
42C577860.03
51B575560.03
52D575560.03
61C578800.02
62D578800.02
LS refinement shellResolution: 3.3→3.383 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 206 -
Rwork0.389 3899 -
all-4105 -
obs--99.85 %

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