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- PDB-3c2w: Crystal structure of the photosensory core domain of P. aeruginos... -

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Basic information

Entry
Database: PDB / ID: 3c2w
TitleCrystal structure of the photosensory core domain of P. aeruginosa bacteriophytochrome PaBphP in the Pfr state
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / Knot structure / Chromophore / Kinase / Phosphoprotein / Photoreceptor protein / Receptor / Sensory transduction / 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 / photoreceptor activity / protein kinase activator activity / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
PHY domain / Phytochrome / : / GAF domain / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain ...PHY domain / Phytochrome / : / 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, 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 / Bacteriophytochrome
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsYang, X. / Kuk, J. / Moffat, K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: photoconversion and signal transduction.
Authors: Yang, X. / Kuk, J. / Moffat, K.
History
DepositionJan 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Apr 3, 2024Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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
B: Bacteriophytochrome
C: Bacteriophytochrome
D: Bacteriophytochrome
E: Bacteriophytochrome
F: Bacteriophytochrome
G: Bacteriophytochrome
H: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,24716
Polymers454,5868
Non-polymers4,6618
Water54030
1
E: Bacteriophytochrome
F: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-58 kcal/mol
Surface area41810 Å2
MethodPISA
2
C: Bacteriophytochrome
D: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-51 kcal/mol
Surface area43080 Å2
MethodPISA
3
G: Bacteriophytochrome
H: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint-54 kcal/mol
Surface area43220 Å2
MethodPISA
4
A: Bacteriophytochrome
B: Bacteriophytochrome
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,8124
Polymers113,6462
Non-polymers1,1652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-47 kcal/mol
Surface area42400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.417, 164.255, 434.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56823.230 Da / Num. of mol.: 8 / Fragment: photosensory core domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: bphP, PA4117 / Plasmid: pET24a / 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.: 8 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.45M (NH4)H2PO4 0.1M Tris HCl 10mg/ml protein, pH 7.7, 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: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 150452 / Num. obs: 89068 / % possible obs: 59.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 70.12 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.4 / % possible all: 100

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Processing

Software
NameClassification
HKL-3000data collection
SHARPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A partial model built from a mutant structure determined by MAD phasing

Resolution: 2.9→14.996 Å / SU ML: 0.4 / Isotropic thermal model: TLS / Phase error: 36.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2832 4371 5 %
Rwork0.2188 --
obs0.2221 87377 72.1 %
all-121194 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.335 Å2 / ksol: 0.259 e/Å3
Displacement parametersBiso mean: 126.92 Å2
Baniso -1Baniso -2Baniso -3
1-22.401 Å20 Å2-0 Å2
2--18.381 Å2-0 Å2
3----40.782 Å2
Refinement stepCycle: LAST / Resolution: 2.9→14.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30117 0 344 30 30491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531166
X-RAY DIFFRACTIONf_angle_d1.08942329
X-RAY DIFFRACTIONf_dihedral_angle_d17.55411424
X-RAY DIFFRACTIONf_chiral_restr0.0744622
X-RAY DIFFRACTIONf_plane_restr0.0045538
LS refinement shellResolution: 2.9→2.93 Å
RfactorNum. reflection% reflection
Rfree0.48 38 -
Rwork0.383 742 -
obs--20 %
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)
1-0.64530.37690.1370.4707-0.1321.55330.0724-0.0665-0.0044-0.02350.19680.0744-0.1084-0.0468-0.25580.2329-0.0123-0.05220.49950.11110.4376-17.854218.081898.2925
20.4068-0.0590.17860.8752-0.00310.674-0.0617-0.2259-0.2427-0.11030.23030.31880.1311-0.2608-0.17210.5097-0.2299-0.22320.69030.25810.7397-40.3775-7.621784.0241
30.3655-0.29140.12260.90160.93791.7505-0.0635-0.07050.0637-0.06850.1655-0.04510.0407-0.1238-0.08240.4811-0.0682-0.08080.4182-0.0310.4958-41.555860.422665.8867
40.00540.1715-0.07040.48670.09540.80580.2013-0.07980.01560.0582-0.03240.09320.1296-0.4352-0.14070.4859-0.2675-0.21110.8790.28810.6868-70.972237.475566.4169
50.67590.2762-0.0250.08470.43040.77370.03860.2575-0.0298-0.17930.12280.0869-0.36760.4935-0.06290.8486-0.2225-0.22190.92160.18010.6515-50.250660.808311.1766
60.56730.01110.19810.61310.23940.61870.23920.0065-0.0418-0.1827-0.17980.00480.0348-0.0742-0.0460.7091-0.0851-0.17660.53290.12260.4065-77.926338.32421.3324
70.81080.0667-0.47630.328-0.34841.4680.07140.0177-0.0964-0.3361-0.0487-0.03210.25980.0572-00.5872-0.05240.10320.23290.00030.3512-12.543932.270345.3371
80.62330.0655-0.2594-0.11210.08461.19520.06250.1388-0.0272-0.15070.0397-0.11450.5789-0.1893-0.13941.0042-0.2134-0.34420.43660.15160.664-36.21523.971639.6967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA5 - 900
2X-RAY DIFFRACTION2chain BB5 - 900
3X-RAY DIFFRACTION3chain CC5 - 900
4X-RAY DIFFRACTION4chain DD5 - 900
5X-RAY DIFFRACTION5chain EE5 - 900
6X-RAY DIFFRACTION6chain FF5 - 900
7X-RAY DIFFRACTION7chain GG5 - 900
8X-RAY DIFFRACTION8chain HH5 - 900

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