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- PDB-4r6l: Crystal structure of bacteriophytochrome RpBphP2 from photosynthe... -

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Basic information

Entry
Database: PDB / ID: 4r6l
TitleCrystal structure of bacteriophytochrome RpBphP2 from photosynthetic bacterium R. palustris
ComponentsBacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
KeywordsSIGNALING PROTEIN / PAS fold / photoreceptor / response regulator RPA3017 / TRANSFERASE
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 / protein kinase activator activity / photoreceptor activity / regulation of DNA-templated transcription / ATP binding / metal ion 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. / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / 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
BILIVERDINE IX ALPHA / histidine kinase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.395 Å
AuthorsYang, X. / Stojkovic, E. / Ozarowski, W. / Kuk, J. / Davydova, E. / Moffat, K.
CitationJournal: Structure / Year: 2015
Title: Light Signaling Mechanism of Two Tandem Bacteriophytochromes.
Authors: Yang, X. / Stojkovic, E.A. / Ozarowski, W.B. / Kuk, J. / Davydova, E. / Moffat, K.
History
DepositionAug 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
B: Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,7944
Polymers113,6292
Non-polymers1,1652
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-49 kcal/mol
Surface area44920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.396, 174.396, 95.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1


Mass: 56814.555 Da / Num. of mol.: 2 / Fragment: photosensory core module, UNP residues 1-506
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: CGA009 / Gene: phyB1, RPA3015 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6N5G3
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
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: 3.81 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10mg/ml protein, 12% polyacrylic acid, 0.1M MgCl2, 0.1M Hepes (pH7.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 8, 2009
RadiationMonochromator: diamond laue monochromators / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.306→50 Å / Num. obs: 22049 / % possible obs: 62 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 15

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OOL

2ool


Resolution: 3.395→49.021 Å / SU ML: 0.66 / σ(F): 1.34 / Phase error: 41.64 / Stereochemistry target values: ML
Details: Author states that issues with the main chain geometry and the high B-factors are largely due to the poor resolution.
RfactorNum. reflection% reflection
Rfree0.3219 1119 5.09 %
Rwork0.2677 --
obs0.2704 21991 95.3 %
all-25592 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.395→49.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 86 0 7198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097356
X-RAY DIFFRACTIONf_angle_d1.90210016
X-RAY DIFFRACTIONf_dihedral_angle_d19.8832693
X-RAY DIFFRACTIONf_chiral_restr0.0751129
X-RAY DIFFRACTIONf_plane_restr0.0111311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3951-3.54960.43031070.35662017X-RAY DIFFRACTION74
3.5496-3.73670.42631390.35732474X-RAY DIFFRACTION92
3.7367-3.97070.41261380.34592721X-RAY DIFFRACTION99
3.9707-4.27710.35631430.31122693X-RAY DIFFRACTION100
4.2771-4.70730.32531350.27342736X-RAY DIFFRACTION100
4.7073-5.38770.33561550.27032723X-RAY DIFFRACTION100
5.3877-6.7850.36371620.3092728X-RAY DIFFRACTION100
6.785-49.02650.23421400.1962780X-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)
11.1946-0.10411.97320.7202-0.54436.2774-0.190.035-0.046-0.10740.1059-0.1867-0.05670.174200.9886-0.31440.07461.1155-0.08881.219758.2518-73.10496.542
24.84092.15290.32471.51190.04893.66320.14840.2071-0.36940.2214-0.01870.2763-0.0893-0.18710.00011.5181-0.10670.13471.08090.07261.528849.9776-42.336418.2983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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