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- PDB-3ibr: Crystal Structure of P. aeruginosa Bacteriophytochrome Photosenso... -

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Basic information

Entry
Database: PDB / ID: 3ibr
TitleCrystal Structure of P. aeruginosa Bacteriophytochrome Photosensory Core Module Mutant Q188L in the Mixed Pr/Pfr State
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / phytochrome / red-light photoreceptor / photoconversion / chromophore / ATP-binding / Kinase / Nucleotide-binding / Phosphoprotein / Photoreceptor protein / Receptor / Sensory transduction
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 / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / Phytochrome chromophore attachment domain ...PHY domain / : / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / GAF domain / 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, 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 / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Bacteriophytochrome
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å
AuthorsYang, X. / Kuk, J. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome.
Authors: Yang, X. / Kuk, J. / Moffat, K.
History
DepositionJul 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,9074
Polymers114,7422
Non-polymers1,1652
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-44 kcal/mol
Surface area42910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.902, 108.902, 188.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 57371.004 Da / Num. of mol.: 2 / Fragment: UNP residues 1-497 / Mutation: Q188L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21/DE3 / References: UniProt: Q9HWR3, histidine kinase
#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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: protein: 10mg/ml, 0.5% PEG4000 (w/v), 0.01M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2007
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. all: 24681 / Num. obs: 23250 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.7
Reflection shellResolution: 2.97→3.04 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.3 / % possible all: 80.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.97→37.74 Å / SU ML: 0.52 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.307 1128 5.1 %
Rwork0.233 --
obs0.236 22136 84.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 72.07 Å2 / ksol: 0.29 e/Å3
Refinement stepCycle: LAST / Resolution: 2.97→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 0 86 2 7290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077720
X-RAY DIFFRACTIONf_angle_d1.33610513
X-RAY DIFFRACTIONf_dihedral_angle_d18.2712811
X-RAY DIFFRACTIONf_chiral_restr0.0751127
X-RAY DIFFRACTIONf_plane_restr0.0051372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.97-3.10510.3744520.3441240X-RAY DIFFRACTION40
3.1051-3.26880.35171040.32742007X-RAY DIFFRACTION66
3.2688-3.47340.41231300.29382619X-RAY DIFFRACTION84
3.4734-3.74140.34881740.25463045X-RAY DIFFRACTION98
3.7414-4.11750.30041550.24513033X-RAY DIFFRACTION98
4.1175-4.71230.26761680.20453036X-RAY DIFFRACTION98
4.7123-5.93330.32471640.21833044X-RAY DIFFRACTION98
5.9333-37.74760.2741810.20762984X-RAY DIFFRACTION96
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined2.15860.0964-0.71980.0371-0.31730.9584-0.0769-0.35730.75450.24150.1636-0.2064-0.2560.3333-0.09230.338-0.0751-0.14620.2748-0.26690.469129.417623.244117.2541
20.6861-0.31330.34161.0182-0.51950.88560.12590.1588-0.2856-0.22740.01560.33170.502-0.059-0.14390.5653-0.1063-0.11340.4194-0.12890.5591
Refinement TLS groupSelection details: CHAIN B

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