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- PDB-5zoh: Crystal structure of a far-red light-absorbing form of AnPixJg2_B... -

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Basic information

Entry
Database: PDB / ID: 5zoh
TitleCrystal structure of a far-red light-absorbing form of AnPixJg2_BV4 in complex with biliverdin
ComponentsMethyl-accepting chemotaxis proteinMethyl-accepting chemotaxis proteins
KeywordsSIGNALING PROTEIN / Photoreceptor / Cyanobacteriochrome / Complex / Tetrapyrrole / Biliverdin
Function / homology
Function and homology information


chemotaxis / transmembrane signaling receptor activity / signal transduction / membrane
Similarity search - Function
Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. ...Chemotaxis methyl-accepting receptor / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Methyl-accepting chemotaxis protein (MCP) signalling domain / Methyl-accepting chemotaxis protein (MCP) signalling domain / Bacterial chemotaxis sensory transducers domain profile. / Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). / GAF domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BILIVERDINE IX ALPHA / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMiyazaki, T. / Fushimi, K. / Narikawa, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Science and Technology Japan
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Rational conversion of chromophore selectivity of cyanobacteriochromes to accept mammalian intrinsic biliverdin.
Authors: Fushimi, K. / Miyazaki, T. / Kuwasaki, Y. / Nakajima, T. / Yamamoto, T. / Suzuki, K. / Ueda, Y. / Miyake, K. / Takeda, Y. / Choi, J.H. / Kawagishi, H. / Park, E.Y. / Ikeuchi, M. / Sato, M. / Narikawa, R.
History
DepositionApr 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3163
Polymers22,6411
Non-polymers6752
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-18 kcal/mol
Surface area9950 Å2
2
A: Methyl-accepting chemotaxis protein
hetero molecules

A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6326
Polymers45,2832
Non-polymers1,3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5560 Å2
ΔGint-52 kcal/mol
Surface area17260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.957, 60.650, 55.475
Angle α, β, γ (deg.)90.00, 108.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methyl-accepting chemotaxis protein / Methyl-accepting chemotaxis proteins / Cyanobacteriochrome


Mass: 22641.479 Da / Num. of mol.: 1 / Mutation: H293Y, F308T, H318Y, I336V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / SAG 25.82 / UTEX 2576 / Gene: all1069 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q8YXY7
#2: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1 M sodium cacodylate, 26% PEG 3350, 0.2 M ammonium sulfate
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 27039 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 28.2
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 2737 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W2Z

3w2z


Resolution: 1.6→31.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 1.881 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.098 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24075 1346 5 %RANDOM
Rwork0.20607 ---
obs0.20785 25495 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.308 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.01 Å2
2--0.01 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.6→31.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 49 89 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021519
X-RAY DIFFRACTIONr_bond_other_d0.0040.021410
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.9652071
X-RAY DIFFRACTIONr_angle_other_deg0.88533234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.99524.38473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12915252
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.113158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021722
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02371
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_it2.1622.425703
X-RAY DIFFRACTIONr_mcbond_other2.1362.42702
X-RAY DIFFRACTIONr_mcangle_it3.5013.62879
X-RAY DIFFRACTIONr_mcangle_other3.4993.624880
X-RAY DIFFRACTIONr_scbond_it2.4122.714816
X-RAY DIFFRACTIONr_scbond_other2.4022.714816
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9263.9421189
X-RAY DIFFRACTIONr_long_range_B_refined6.17620.3871912
X-RAY DIFFRACTIONr_long_range_B_other6.11920.271892
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 111 -
Rwork0.258 1885 -
obs--99.11 %

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