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- PDB-3nop: Light-induced intermediate structure L1 of Pseudomonas aeruginosa... -

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Basic information

Entry
Database: PDB / ID: 3nop
TitleLight-induced intermediate structure L1 of Pseudomonas aeruginosa bacteriophytochrome
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / intermediate structure / chromophore binding pocket / difference Fourier method
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 / photoreceptor activity / phosphorelay sensor kinase 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 / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / GAF domain ...PHY domain / Phytochrome / 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 / 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 / Bacteriophytochrome
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / difference Fourier Method / Resolution: 2.8 Å
AuthorsYang, X. / Ren, Z. / Moffat, K.
CitationJournal: Nature / Year: 2011
Title: Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome.
Authors: Yang, X. / Ren, Z. / Kuk, J. / Moffat, K.
History
DepositionJun 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 6, 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

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Assembly

Deposited unit
C: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4062
Polymers56,8231
Non-polymers5831
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)154.380, 162.979, 436.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.95018, -0.18163, -0.25332), (0.10224, 0.94933, -0.29717), (0.29446, 0.25647, 0.92061)49.36829, -15.39839, 34.53864
3generate(-0.60638, -0.18951, -0.77226), (-0.16908, -0.91825, 0.3581), (-0.77699, 0.34772, 0.52476)-2.77281, 16.08975, -3.4757
4generate(-0.8218, -0.23836, -0.51752), (-0.17992, -0.75325, 0.63264), (-0.54062, 0.61302, 0.57614)-56.34828, 32.87178, -30.58517
5generate(0.15383, 0.96949, -0.19088), (0.97132, -0.18382, -0.15084), (-0.18132, -0.1622, -0.96996)-88.86876, 121.50987, 77.39897
6generate(-0.27819, -0.88393, 0.37588), (-0.67277, -0.09999, -0.73307), (0.68556, -0.45681, -0.56686)-61.45194, 64.605, 113.99367
7generate(0.02487, 0.99475, 0.09932), (0.99438, -0.03484, 0.09999), (0.10292, 0.09627, -0.99002)-77.39406, 68.65884, 109.27385
8generate(-0.25693, -0.69027, 0.6764), (-0.86451, -0.14869, -0.48012), (0.43198, -0.70811, -0.55854)-49.73023, 8.51341, 136.80702

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 56823.230 Da / Num. of mol.: 1
Fragment: N-terminal photosensory core module, UNP residues 1-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HWR3, histidine kinase
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6

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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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.7
Details: 10mg/ml protein, 0.1M Tris HCl buffer, 0.45M ammonium phosphate, pH 7.7, VAPOR DIFFUSION, 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2008
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 158473 / Num. obs: 131216 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.118

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Processing

Software
NameClassification
HKL-2000data collection
DynamiXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: difference Fourier Method
Starting model: PDB ENTRY 3NHQ

3nhq


Resolution: 2.8→50 Å / Num. reflection all: 15473 / Num. reflection obs: 131216 / Occupancy max: 1 / Occupancy min: 0.56 / Cross valid method: real space correlation coefficient / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: This cryo-trapped structure was determined based on difference Fourier method. The L1 (3NOP), L2(3NOT) and L3(3NOU) structures were refined jointly in real space against a set of (Flight- ...Details: This cryo-trapped structure was determined based on difference Fourier method. The L1 (3NOP), L2(3NOT) and L3(3NOU) structures were refined jointly in real space against a set of (Flight-Fdark) difference maps representing mixtures of the L1, L2 and L3 structures in variable relative concentrations using software DynamiX. DynamiX is a collection of software tools for analyzing dynamic crystallographic data developed by Zhong Ren. Algorithms and methods are described in Ren, Z et al. Resolution of structural heterogeneity in dynamic and static crystallography. Manuscript in preparation.
Displacement parametersBiso max: 167.38 Å2 / Biso min: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3817 0 43 0 3860

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