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- PDB-3nhq: The dark Pfr structure of the photosensory core module of P. aeru... -

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Basic information

Entry
Database: PDB / ID: 3nhq
TitleThe dark Pfr structure of the photosensory core module of P. aeruginosa Bacteriophytochrome
ComponentsBacteriophytochrome
KeywordsSIGNALING PROTEIN / Photoreceptor / phytochrome / PAS / signaling
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 / 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: 2.55 Å
AuthorsYang, X. / Ren, Z. / Kuk, J. / Moffat, K.
Citation
Journal: Nature / Year: 2011
Title: Temperature-scan cryocrystallography reveals reaction intermediates in bacteriophytochrome.
Authors: Yang, X. / Ren, Z. / Kuk, J. / Moffat, K.
#1: Journal: 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
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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
Revision 1.2Nov 6, 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
Water3,621201
1
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 area6480 Å2
ΔGint-50 kcal/mol
Surface area42050 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 area6570 Å2
ΔGint-53 kcal/mol
Surface area42860 Å2
MethodPISA
3
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 area6660 Å2
ΔGint-52 kcal/mol
Surface area42240 Å2
MethodPISA
4
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 area6630 Å2
ΔGint-55 kcal/mol
Surface area43050 Å2
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

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Components

#1: Protein
Bacteriophytochrome / Phytochrome-like protein


Mass: 56823.230 Da / Num. of mol.: 8 / Fragment: Photosensory Core Module (UNP Residue 1-497)
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
#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.: 201 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.7
Details: 10mg/ml protein, 0.45 M ammonium phosphate, 0.1 M Tris-HCl, 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: RAYONIX MX-300 / Detector: CCD / Date: Feb 19, 2009 / Details: C(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 188239 / Num. obs: 148709 / % possible obs: 79 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 23
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 1.7 / % possible all: 29.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C2W

3c2w


Resolution: 2.55→48.48 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 33.36 / Stereochemistry target values: ML
Details: The refinement was facilitated by an automated real space refinement procedure that optimizes main chain torsional angles. Reference: Haddadian et al. Automated real-space refinement of ...Details: The refinement was facilitated by an automated real space refinement procedure that optimizes main chain torsional angles. Reference: Haddadian et al. Automated real-space refinement of protein structures using a realistic backbone move set. Biophysical Journal. In press.
RfactorNum. reflection% reflection
Rfree0.2579 7389 5.01 %
Rwork0.2152 --
obs0.2174 147602 82.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.16 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.2222 Å20 Å2-0 Å2
2--7.17 Å20 Å2
3----17.3922 Å2
Refinement stepCycle: LAST / Resolution: 2.55→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30240 0 344 201 30785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431298
X-RAY DIFFRACTIONf_angle_d0.86842488
X-RAY DIFFRACTIONf_dihedral_angle_d15.97911535
X-RAY DIFFRACTIONf_chiral_restr0.0554642
X-RAY DIFFRACTIONf_plane_restr0.0035565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.5790.3964870.34581591X-RAY DIFFRACTION29
2.579-2.60930.42161100.33861872X-RAY DIFFRACTION33
2.6093-2.64110.39091190.34432153X-RAY DIFFRACTION39
2.6411-2.67460.36811210.34182437X-RAY DIFFRACTION43
2.6746-2.70980.40041450.33322672X-RAY DIFFRACTION48
2.7098-2.74690.38581400.33632955X-RAY DIFFRACTION52
2.7469-2.78610.3881640.33163290X-RAY DIFFRACTION59
2.7861-2.82770.4011770.32633610X-RAY DIFFRACTION64
2.8277-2.87190.34552100.31014079X-RAY DIFFRACTION72
2.8719-2.9190.38382430.31114354X-RAY DIFFRACTION78
2.919-2.96930.41022460.30074746X-RAY DIFFRACTION85
2.9693-3.02330.33992840.29945093X-RAY DIFFRACTION91
3.0233-3.08140.3372790.28955362X-RAY DIFFRACTION96
3.0814-3.14430.36392940.2795565X-RAY DIFFRACTION99
3.1443-3.21270.33072880.27245589X-RAY DIFFRACTION100
3.2127-3.28740.32312770.27025639X-RAY DIFFRACTION100
3.2874-3.36960.29952940.26325585X-RAY DIFFRACTION100
3.3696-3.46060.2763040.24695610X-RAY DIFFRACTION100
3.4606-3.56240.28983230.23545604X-RAY DIFFRACTION100
3.5624-3.67740.28353080.21975609X-RAY DIFFRACTION100
3.6774-3.80880.27552720.215625X-RAY DIFFRACTION100
3.8088-3.96120.23322860.19545689X-RAY DIFFRACTION100
3.9612-4.14140.20622850.17235653X-RAY DIFFRACTION100
4.1414-4.35960.19542840.15215642X-RAY DIFFRACTION100
4.3596-4.63250.19353120.15155650X-RAY DIFFRACTION100
4.6325-4.98990.19993170.15715606X-RAY DIFFRACTION100
4.9899-5.49140.22223030.17025688X-RAY DIFFRACTION100
5.4914-6.28460.2322720.19985758X-RAY DIFFRACTION100
6.2846-7.91240.23313240.19165710X-RAY DIFFRACTION100
7.9124-48.48840.18463210.17055777X-RAY DIFFRACTION97
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)
1-0.0780.292-0.34850.4296-0.2411.91570.11940.00970.0060.04310.08310.01630.004-0.0459-0.18290.16090.0676-0.03430.2540.06360.2993-17.700717.867298.4831
20.8693-0.30760.28830.93480.0570.89940.0776-0.2069-0.2599-0.11750.11220.30170.1707-0.2837-0.19830.259-0.1681-0.15970.28690.19130.3905-40.1405-7.8284.0241
30.6148-0.23-0.08750.84380.71551.106-0.0053-0.03910.08830.06490.1188-0.05680.0015-0.0173-0.08340.26590.0656-0.07960.0993-0.00870.2179-41.345559.92866.0257
40.65430.26070.12330.80940.16121.08230.1394-0.1685-0.04880.08630.02960.17230.1258-0.4286-0.16340.3803-0.0922-0.13940.51590.23310.4288-70.681736.976566.5316
50.69530.28150.1920.14130.13642.0292-0.03740.2880.0337-0.12180.09840.081-0.33330.42650.00880.3695-0.0819-0.20560.37650.15130.2764-49.739460.266911.1614
60.63340.05670.38791.08510.44441.0850.10060.0506-0.1175-0.2354-0.03640.00070.1404-0.085-0.05910.4647-0.0615-0.09830.26870.04560.2421-77.519737.939321.1216
70.45830.1056-0.3730.9212-0.08341.38880.05930.04260.0007-0.3072-0.0247-0.10520.05310.0879-0.01650.26890.05720.0750.18320.03480.2068-12.325932.05645.4875
80.47210.1019-0.07840.2408-0.42621.34940.13460.1999-0.0932-0.37780.0259-0.01460.4273-0.1803-0.14470.8254-0.1186-0.28970.36050.06380.4793-35.84633.812139.6799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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