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- PDB-4z1w: CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y... -

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Basic information

Entry
Database: PDB / ID: 4z1w
TitleCRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y263F From Synchrotron
ComponentsBacteriophytochrome
KeywordsTRANSFERASE / BACTERIOPHYTOCHROME / PAS / GAF / BILIVERDIN / SIGNALING PROTEIN
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
: / GAF domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain ...: / GAF domain / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / PAS domain / Signal transduction histidine kinase-related protein, C-terminal / 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
Chem-LBV / Chem-LBW / Bacteriophytochrome
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBhattacharya, S. / Satyshur, K.A. / Wangkanont, K. / Lehtivuori, H. / Forest, K.T.
Funding support United States, Finland, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
National Science Foundation (NSF, United States)1518160 United States
Academy of Finland277194 Finland
CitationJournal: Front Mol Biosci / Year: 2015
Title: Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor.
Authors: Lehtivuori, H. / Bhattacharya, S. / Angenent-Mari, N.M. / Satyshur, K.A. / Forest, K.T.
History
DepositionMar 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.country / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3553
Polymers37,1831
Non-polymers1,1712
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.434, 53.340, 65.690
Angle α, β, γ (deg.)90.00, 90.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-638-

HOH

21A-707-

HOH

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Components

#1: Protein Bacteriophytochrome / Phytochrome-like protein


Mass: 37183.344 Da / Num. of mol.: 1 / Mutation: F145S,D207L Y263F, L311E, L314E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: bphP, DR_A0050 / Plasmid: PET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q9RZA4, histidine kinase
#2: Chemical ChemComp-LBV / 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid / 2(R),3(E)- PHYTOCHROMOBILIN


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#3: Chemical ChemComp-LBW / 3-[2-[(Z)-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-pyrrol-1-ium-2-ylidene]methyl]-5-[(Z)-[(3E,4R)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 585.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37N4O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 46.76 % / Description: Green prismatic crystals.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0.
PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.3→23.8 Å / Num. obs: 77741 / % possible obs: 96.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 8.8 Å2 / Rsym value: 0.052 / Net I/σ(I): 33.2
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S7Q, 4O8G

3s7q

4o8g


Resolution: 1.3→23.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.146 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16019 3829 4.9 %RANDOM
Rwork0.14455 ---
obs0.14531 73911 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å2-0.71 Å2
2--0.59 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→23.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 86 231 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0192723
X-RAY DIFFRACTIONr_bond_other_d0.0020.022653
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0153750
X-RAY DIFFRACTIONr_angle_other_deg0.8713.0016038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83523.394109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35315412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6791520
X-RAY DIFFRACTIONr_chiral_restr0.0690.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02602
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_it0.7521.4851338
X-RAY DIFFRACTIONr_mcbond_other0.7511.4821337
X-RAY DIFFRACTIONr_mcangle_it0.8842.221689
X-RAY DIFFRACTIONr_mcangle_other0.8842.2231690
X-RAY DIFFRACTIONr_scbond_it0.9451.6841385
X-RAY DIFFRACTIONr_scbond_other0.9441.6831386
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.052.4542057
X-RAY DIFFRACTIONr_long_range_B_refined1.77812.2763042
X-RAY DIFFRACTIONr_long_range_B_other1.47911.8612934
X-RAY DIFFRACTIONr_rigid_bond_restr0.96835376
X-RAY DIFFRACTIONr_sphericity_free21.125571
X-RAY DIFFRACTIONr_sphericity_bonded4.37655450
LS refinement shellResolution: 1.298→1.332 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 256 -
Rwork0.151 5193 -
obs--92.7 %

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