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- PDB-5c5k: Structure of the Pfr form of a canonical phytochrome -

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Basic information

Entry
Database: PDB / ID: 5c5k
TitleStructure of the Pfr form of a canonical phytochrome
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / photosensor
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
ACETATE ION / beta-D-glucopyranose / BILIVERDINE IX ALPHA / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.31 Å
AuthorsBurgie, E.S. / Vierstra, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1329956 United States
CitationJournal: Structure / Year: 2016
Title: Crystal Structure of Deinococcus Phytochrome in the Photoactivated State Reveals a Cascade of Structural Rearrangements during Photoconversion.
Authors: Burgie, E.S. / Zhang, J. / Vierstra, R.D.
History
DepositionJun 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Bacteriophytochrome
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,56511
Polymers226,9334
Non-polymers2,6327
Water32418
1
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7536
Polymers113,4662
Non-polymers1,2864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-49 kcal/mol
Surface area40800 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8125
Polymers113,4662
Non-polymers1,3453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-41 kcal/mol
Surface area41040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.399, 192.747, 225.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56733.230 Da / Num. of mol.: 4 / Fragment: residues 1-502 / Mutation: F469W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RZA4, histidine kinase
#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 24 molecules

#2: Chemical
ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 4.28 Å3/Da / Density % sol: 71.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 3350, sodium chloride, ethylene glycol, MOPS, ammonium acetate, fructose, glucose, sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 6, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.31→48.8 Å / Num. obs: 55199 / % possible obs: 99.8 % / Redundancy: 20.6 % / Biso Wilson estimate: 116.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.242 / Rpim(I) all: 0.054 / Net I/σ(I): 22.4 / Num. measured all: 1137231 / Scaling rejects: 1557
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
3.31-3.4821.13.6161.49409944640.4690.79399.6
14.34-48.815.50.056124.9125758120.9970.01596.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O9C and 4Q0J

2o9c

4q0j


Resolution: 3.31→48.8 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1884 3.64 %
Rwork0.1963 --
obs0.1976 51713 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.31→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14715 0 192 18 14925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215337
X-RAY DIFFRACTIONf_angle_d0.60221010
X-RAY DIFFRACTIONf_dihedral_angle_d16.1769113
X-RAY DIFFRACTIONf_chiral_restr0.0382349
X-RAY DIFFRACTIONf_plane_restr0.0042738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3097-3.39920.427310.3602737X-RAY DIFFRACTION17
3.3992-3.49910.3542880.31842243X-RAY DIFFRACTION52
3.4991-3.61210.32441270.29013321X-RAY DIFFRACTION77
3.6121-3.74110.33941560.28424159X-RAY DIFFRACTION96
3.7411-3.89080.26171630.25494301X-RAY DIFFRACTION100
3.8908-4.06780.23061610.21674309X-RAY DIFFRACTION100
4.0678-4.28220.21091630.1974302X-RAY DIFFRACTION100
4.2822-4.55030.19621630.17764334X-RAY DIFFRACTION100
4.5503-4.90130.21961630.17414327X-RAY DIFFRACTION100
4.9013-5.3940.22571640.18944365X-RAY DIFFRACTION100
5.394-6.17320.28031650.21414393X-RAY DIFFRACTION100
6.1732-7.77250.23811680.20524444X-RAY DIFFRACTION100
7.7725-48.80510.19321720.15654594X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81960.07360.29653.0038-1.53297.03350.2901-0.3695-0.24570.4174-0.0503-0.13230.35270.0613-0.22590.5644-0.10490.0140.7346-0.00750.439715.839-38.871112.6437
23.958-3.98260.84898.6052-3.21562.38030.36810.35521.03350.2160.01630.0667-0.8067-0.6037-0.42861.02060.20110.19171.2150.17220.80953.1662-8.005-8.3704
34.83581.80830.4896.6189-1.45765.41570.22930.6896-0.2399-0.6659-0.1788-0.02490.2504-0.0053-0.08020.69550.12180.02561.20590.15570.296835.9787-40.1871-25.5499
41.51290.76370.22784.51911.11621.84250.4604-0.29080.65640.1317-0.3498-0.1085-0.86710.3216-0.11451.0054-0.16340.26781.15970.04070.721444.7223-14.9477-1.2182
56.29493.86652.867.2294.50886.53490.0278-0.2736-0.09320.44460.17990.72930.0771-1.1997-0.16331.08050.35030.23741.57620.92371.6976-20.47962.7384-31.4699
61.20790.7179-0.26623.9701-0.47225.6244-0.03050.14340.1809-0.35690.78910.8681-0.8812-0.4664-0.76511.09750.19640.21661.80150.91011.8288-15.738210.5598-48.7625
78.77593.3935-3.62223.9882-2.34694.0536-0.1273-0.5266-0.34370.03030.56110.4488-0.24860.12-0.37141.2054-0.14220.0261.31310.41770.738813.753718.7439-64.9148
81.9554-0.3837-0.15942.90381.05673.6007-0.0673-0.2513-0.4036-0.24030.3890.89480.7125-0.448-0.25081.6516-0.5061-0.44151.77070.82741.7595-13.9281-18.435-71.9392
96.2038-1.49273.07763.2977-2.17234.1056-0.63440.70280.5394-0.76270.48430.56510.24360.37590.08151.35330.1401-0.03571.54850.5470.920419.3518-19.8697-50.5879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 502 )
3X-RAY DIFFRACTION3chain 'B' and (resid 7 through 136 )
4X-RAY DIFFRACTION4chain 'B' and (resid 137 through 502 )
5X-RAY DIFFRACTION5chain 'C' and (resid 7 through 109 )
6X-RAY DIFFRACTION6chain 'C' and (resid 110 through 298 )
7X-RAY DIFFRACTION7chain 'C' and (resid 299 through 503 )
8X-RAY DIFFRACTION8chain 'D' and (resid 7 through 298 )
9X-RAY DIFFRACTION9chain 'D' and (resid 299 through 502 )

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