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- PDB-5hsq: The surface engineered photosensory module (PAS-GAF-PHY) of the b... -

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Basic information

Entry
Database: PDB / ID: 5hsq
TitleThe surface engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A.
ComponentsBacteriophytochrome protein
KeywordsSIGNALING PROTEIN / surface mutations / bilin chromophore / photoisomerization
Function / homology
Function and homology information


red or far-red light photoreceptor activity / red, far-red light phototransduction / protein histidine kinase activity / detection of visible light / histidine kinase / phosphorelay sensor kinase activity / regulation of DNA-templated transcription
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 / IMIDAZOLE / histidine kinase
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNagano, S. / Scheerer, P. / Zubow, K. / Lamparter, T. / Krauss, N.
Funding support United Kingdom, Germany, 3items
OrganizationGrant numberCountry
Queen Mary University of LondonPostgraduate Research Studentship United Kingdom
German Research FoundationSFB498-B2 Germany
German Research FoundationSFB1078-B6 Germany
CitationJournal: J.Biol.Chem. / Year: 2016
Title: The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers.
Authors: Nagano, S. / Scheerer, P. / Zubow, K. / Michael, N. / Inomata, K. / Lamparter, T. / Krau, N.
History
DepositionJan 26, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5215
Polymers54,7371
Non-polymers7844
Water6,287349
1
A: Bacteriophytochrome protein
hetero molecules

A: Bacteriophytochrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,04210
Polymers109,4742
Non-polymers1,5688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area4980 Å2
ΔGint-35 kcal/mol
Surface area40980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.348, 69.348, 236.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-905-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacteriophytochrome protein


Mass: 54736.945 Da / Num. of mol.: 1 / Mutation: E86A, E87A, E336A, K337A
Source method: isolated from a genetically manipulated source
Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry ...Details: The residue numbering in the PDB entry differs from the one shown in this sequence alignment. The first residue in the PDB entry is 'Leu17' in accordance with the sequence for the entry AAT99575 (NCBI). The respective numbering was used in a number of publications on this protein, and we did not change it in this entry for the sake of consistency with published work and because the true N-terminus has not yet been identified at the protein level.
Source: (gene. exp.) Agrobacterium fabrum (bacteria) / Strain: C58 / ATCC 33970 / Gene: Atu1990 / Plasmid: pET21b(+)
Details (production host): The coding sequence of the protein of interest was subcloned using NdeI and XhoI sites of the plasmid.
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7CY45

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Non-polymers , 5 types, 353 molecules

#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 % / Description: Bipyramidal
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 20% glycerol, 10% PEG8000, 0.05 M MES, 0.05 M imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0718 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 1.85→34.67 Å / Num. all: 49518 / Num. obs: 49518 / % possible obs: 98.6 % / Redundancy: 4.8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.2
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2)9C, 2VEA (PHY domain)

2vea


Resolution: 1.85→34.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.454 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22371 2528 5.1 %RANDOM
Rwork0.18269 ---
obs0.18474 46971 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.842 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---0.93 Å20 Å2
3---1.86 Å2
Refinement stepCycle: 1 / Resolution: 1.85→34.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3715 0 55 349 4119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193988
X-RAY DIFFRACTIONr_bond_other_d0.0030.023817
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9695443
X-RAY DIFFRACTIONr_angle_other_deg1.153.0028784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88923.567171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13115656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7851530
X-RAY DIFFRACTIONr_chiral_restr0.1220.2601
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214591
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02911
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4011.8181995
X-RAY DIFFRACTIONr_mcbond_other1.3981.8171994
X-RAY DIFFRACTIONr_mcangle_it2.2312.7182504
X-RAY DIFFRACTIONr_mcangle_other2.232.7192505
X-RAY DIFFRACTIONr_scbond_it1.8671993
X-RAY DIFFRACTIONr_scbond_other1.8671994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.823.6542923
X-RAY DIFFRACTIONr_long_range_B_refined7.4054756
X-RAY DIFFRACTIONr_long_range_B_other7.3554623
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded18.969512
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 190 -
Rwork0.275 3447 -
obs--99.7 %
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)
10.9753-0.34030.65191.10010.04181.5019-0.17490.1310.12010.2132-0.00380.0819-0.20580.12910.17870.2207-0.0435-0.00390.21020.07380.049114.285-24.5149.057
21.1993-0.7478-0.41970.47730.34921.00320.09510.05390.0219-0.0821-0.0183-0.0144-0.08240.1069-0.07670.1982-0.0302-0.01640.25460.01960.05822.779-32.382-28.734
32.9612-0.2022-0.12930.0747-0.12720.3159-0.053-0.05041.07180.08450.0134-0.1106-0.1587-0.00630.03960.1604-0.0337-0.09520.06530.01010.4254000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 311
2X-RAY DIFFRACTION2A312 - 504
3X-RAY DIFFRACTION3A - C601

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