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- PDB-4o0p: Crystal Structure of D. radiodurans Bacteriophytochrome Photosens... -

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Basic information

Entry
Database: PDB / ID: 4o0p
TitleCrystal Structure of D. radiodurans Bacteriophytochrome Photosensory Core Module in its Dark 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 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 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 14, 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 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET Determination method: Author determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3334
Polymers113,1622
Non-polymers1,1712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-35 kcal/mol
Surface area43170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.280, 150.280, 145.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 4 - 503 / Label seq-ID: 18 - 517

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 56581.027 Da / Num. of mol.: 2 / Fragment: Photosensory Core Module, UNP residues 1-502
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (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.: 2 / 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: 4.2 Å3/Da / Density % sol: 70.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG 1500, in dark, pH 7.0, 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: 0.98044 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: 0.98044 Å / Relative weight: 1
ReflectionResolution: 3.8→48.65 Å / Num. all: 18561 / Num. obs: 18551 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.97 % / Biso Wilson estimate: 130.975 Å2 / Rmerge(I) obs: 0.392 / Rsym value: 0.411 / Net I/σ(I): 4.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique allNum. unique obsRrim(I) allRsym value% possible all
3.8-3.911.60.2094.5131.05157531362136213624.7254.725100
3.9-411.40.253.2451.17145591275127512753.43.4100
4-4.510.70.4511.6921.79502444710471047101.7811.781100
4.5-8110.9420.5055.551012009177917791770.5310.531100
8-1510.90.9930.14912.49187151717171717170.1560.156100
159.60.9920.14712.4829713203103100.1560.15696.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O9C

2o9c


Resolution: 3.8→48.65 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.3487 / WRfactor Rwork: 0.3096 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7726 / SU B: 32.817 / SU ML: 0.502 / SU Rfree: 0.1421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 928 5 %RANDOM
Rwork0.2529 ---
all0.2536 18525 --
obs0.2536 17597 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 355.56 Å2 / Biso mean: 210.2428 Å2 / Biso min: 67.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å2-0 Å2-0 Å2
2---1.8 Å2-0 Å2
3---3.59 Å2
Refinement stepCycle: LAST / Resolution: 3.8→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 86 0 7502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197704
X-RAY DIFFRACTIONr_bond_other_d0.0010.027345
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.98910547
X-RAY DIFFRACTIONr_angle_other_deg0.727316861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.425958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.65623.221326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.352151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0091560
X-RAY DIFFRACTIONr_chiral_restr0.0510.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218708
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021714
X-RAY DIFFRACTIONr_mcbond_it11.63120.7423865
X-RAY DIFFRACTIONr_mcbond_other11.63220.743864
X-RAY DIFFRACTIONr_mcangle_it19.20631.0574812
Refine LS restraints NCSNumber: 7295 / Type: TIGHT THERMAL / Rms dev position: 24.25 Å / Weight position: 0.5
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 70 -
Rwork0.371 1295 -
all-1365 -
obs-1365 99.71 %

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