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- PDB-4s21: Crystal structure of the photosensory core module of bacteriophyt... -

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Basic information

Entry
Database: PDB / ID: 4s21
TitleCrystal structure of the photosensory core module of bacteriophytochrome RPA3015 from R. palustris
ComponentsBacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1
KeywordsSIGNALING PROTEIN / PAS fold / TRANSFERASE
Function / homology
Function and homology information


detection of visible light / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion 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 / His Kinase A (phospho-acceptor) domain ...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 / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / 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
BILIVERDINE IX ALPHA / histidine kinase
Similarity search - Component
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.25 Å
AuthorsYang, X. / Stojkovi, E.A. / Ozarowski, W.B. / 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
DepositionJan 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)115,8814
Polymers114,7162
Non-polymers1,1652
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-50 kcal/mol
Surface area43850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.360, 175.360, 96.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Detailshead-to-head parallel dimer

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Components

#1: Protein Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1 / Photosensory core module of bacteriophytochrome RPA3015 (RpBphP2)


Mass: 57358.082 Da / Num. of mol.: 2 / Fragment: UNP residues 1-505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: CGA009 / Gene: phyB1, RPA3015 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6N5G3
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10mg/ml protein, 1.4M sodium acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 9, 2007
RadiationMonochromator: Si (111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 26837 / Num. obs: 26676 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.048

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Processing

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

2ool


Resolution: 3.25→39.892 Å / SU ML: 0.59 / σ(F): 1.88 / Phase error: 36.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3156 2480 5.04 %
Rwork0.2616 --
obs0.2642 49182 94.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→39.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 86 1 7251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077408
X-RAY DIFFRACTIONf_angle_d1.4810084
X-RAY DIFFRACTIONf_dihedral_angle_d19.8122715
X-RAY DIFFRACTIONf_chiral_restr0.051136
X-RAY DIFFRACTIONf_plane_restr0.0091320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.31250.4304880.38151606X-RAY DIFFRACTION58
3.3125-3.38010.3691110.36542091X-RAY DIFFRACTION77
3.3801-3.45350.40561550.37412407X-RAY DIFFRACTION89
3.4535-3.53380.3451630.34752643X-RAY DIFFRACTION97
3.5338-3.62210.36661370.34712660X-RAY DIFFRACTION97
3.6221-3.720.40311360.34012729X-RAY DIFFRACTION98
3.72-3.82940.33031360.32772705X-RAY DIFFRACTION99
3.8294-3.95290.39421600.31962698X-RAY DIFFRACTION99
3.9529-4.0940.36411270.30882685X-RAY DIFFRACTION98
4.094-4.25780.33171510.28032716X-RAY DIFFRACTION99
4.2578-4.45130.28691390.25032697X-RAY DIFFRACTION99
4.4513-4.68560.27851670.24072697X-RAY DIFFRACTION99
4.6856-4.97870.32461290.24652762X-RAY DIFFRACTION99
4.9787-5.36230.31941730.25872699X-RAY DIFFRACTION99
5.3623-5.90040.37271540.2892733X-RAY DIFFRACTION99
5.9004-6.75060.35411190.29232736X-RAY DIFFRACTION99
6.7506-8.49150.31260.23642710X-RAY DIFFRACTION99
8.4915-39.89510.2081090.17742728X-RAY DIFFRACTION98
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)
12.631-0.31482.8950.7466-0.1959.0207-0.22480.1450.0282-0.1958-0.1413-0.15520.24620.32160.33080.6209-0.60330.07391.10920.05120.993758.5684-73.41376.4303
26.85030.31270.86310.7681-0.41052.64380.7167-0.4455-0.69050.4498-0.55840.0364-0.3014-0.1053-0.151.6848-0.49190.11620.958-0.05081.053350.652-42.540618.0579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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