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- PDB-4o01: Crystal Structure of D. radiodurans Bacteriophytochrome Photosens... -

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Basic information

Entry
Database: PDB / ID: 4o01
TitleCrystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Illuminated Form
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / Phytochrome / Red-Light Photoreceptor / Photoconversion / Chromophore / Sensory Transduction / Signaling Protein / Biliverdin
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / photoreceptor activity / protein kinase activator activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
PHY domain / : / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. ...PHY domain / : / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LBV / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsTakala, H. / Ihalainen, J.A. / Westenhoff, S.
CitationJournal: Nature / Year: 2014
Title: Signal amplification and transduction in phytochrome photosensors
Authors: Takala, H. / Bjorling, A. / Berntsson, O. / Lehtivuori, H. / Niebling, S. / Hoernke, M. / Kosheleva, I. / Henning, R. / Menzel, A. / Ihalainen, J.A. / Westenhoff, S.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: 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_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)228,6678
Polymers226,3244
Non-polymers2,3434
Water00
1
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3334
Polymers113,1622
Non-polymers1,1712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-38 kcal/mol
Surface area40640 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3334
Polymers113,1622
Non-polymers1,1712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-37 kcal/mol
Surface area40410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.900, 195.700, 225.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 1 / Auth seq-ID: 6 - 506 / Label seq-ID: 20 - 520

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.975391, 0.220465, 0.00261), (0.220453, 0.975388, -0.00421), (-0.003474, -0.003531, -0.999988)-42.92259, 4.88589, 6.6754

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Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56581.027 Da / Num. of mol.: 4 / Fragment: Photosensory Core Module, UNP residues 1-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant)
Strain: R1 / Gene: bphP / Plasmid: pET21b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / 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
Has protein modificationY

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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: 4.23 Å3/Da / Density % sol: 70.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, 0.2M NaCl, 25% PEG 3350, sequential 655nm illumination, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98043 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98043 Å / Relative weight: 1
ReflectionResolution: 3.24→49.22 Å / Num. all: 61961 / Num. obs: 61928 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 19.31 % / Biso Wilson estimate: 118.652 Å2 / Rmerge(I) obs: 0.241 / Rsym value: 0.248 / Net I/σ(I): 9.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
3.24-3.3220.34.390.8344954.501100
3.32-3.5202.8791.3181312.953100
3.5-419.11.1773.24160081.209100
4-819.30.24614.33289050.253100
8-1518.10.11927.2236810.123100
1516.50.10527.217080.10895.8

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 3.24→49.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 26.072 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25972 3094 5 %RANDOM
Rwork0.23265 ---
all0.234 61853 --
obs0.234 58759 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 279.15 Å2 / Biso mean: 158.6115 Å2 / Biso min: 80.57 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å2-0 Å2
2---1.75 Å20 Å2
3----3.8 Å2
Refinement stepCycle: LAST / Resolution: 3.24→49.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14784 0 172 0 14956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01915545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214802
X-RAY DIFFRACTIONr_angle_refined_deg1.159221284
X-RAY DIFFRACTIONr_angle_other_deg0.703333959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40251917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58723.185653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.249152270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.87115120
X-RAY DIFFRACTIONr_chiral_restr0.0520.22370
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02117613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023483
X-RAY DIFFRACTIONr_mcbond_it5.7815.5797719
X-RAY DIFFRACTIONr_mcbond_other5.77815.5797718
X-RAY DIFFRACTIONr_mcangle_it9.36923.3549619
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A73106.28
2A731023.9
3A729826.34
4B731022.15
5B729824.66
6C72986.09
LS refinement shellResolution: 3.24→3.324 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 224 -
Rwork0.397 4255 -
all-4479 -
obs--99.98 %

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