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- PDB-6pry: X-ray crystal structure of the blue-light absorbing state of PixJ... -

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Basic information

Entry
Database: PDB / ID: 6pry
TitleX-ray crystal structure of the blue-light absorbing state of PixJ from Thermosynechococcus elongatus by serial femtosecond crystallographic analysis
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / photosensor / photoreversible / GAF domain / bilin / phycoviolobilin
Function / homology
Function and homology information


chemotaxis / lysozyme activity / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Double Cache domain 1 / Cache domain / 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 domain ...Double Cache domain 1 / Cache domain / 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 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
DI(HYDROXYETHYL)ETHER / Phycoviolobilin, blue light-absorbing form / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
Model detailsStructure of photoconvertible TePixJ as Pb
AuthorsBurgie, E.S. / Clinger, J.A. / Miller, M.D. / Phillips Jr., G.N. / Vierstra, R.D. / Orville, A.M. / Kern, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Photoreversible interconversion of a phytochrome photosensory module in the crystalline state.
Authors: Burgie, E.S. / Clinger, J.A. / Miller, M.D. / Brewster, A.S. / Aller, P. / Butryn, A. / Fuller, F.D. / Gul, S. / Young, I.D. / Pham, C.C. / Kim, I.S. / Bhowmick, A. / O'Riordan, L.J. / ...Authors: Burgie, E.S. / Clinger, J.A. / Miller, M.D. / Brewster, A.S. / Aller, P. / Butryn, A. / Fuller, F.D. / Gul, S. / Young, I.D. / Pham, C.C. / Kim, I.S. / Bhowmick, A. / O'Riordan, L.J. / Sutherlin, K.D. / Heinemann, J.V. / Batyuk, A. / Alonso-Mori, R. / Hunter, M.S. / Koglin, J.E. / Yano, J. / Yachandra, V.K. / Sauter, N.K. / Cohen, A.E. / Kern, J. / Orville, A.M. / Phillips Jr., G.N. / Vierstra, R.D.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 11, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyl-accepting chemotaxis protein
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,77211
Polymers34,3052
Non-polymers1,4679
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-47 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.788, 61.417, 116.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Methyl-accepting chemotaxis protein


Mass: 17152.381 Da / Num. of mol.: 2 / Fragment: GAF domain / Mutation: C555A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus BP-1 (bacteria)
Strain: BP-1 / Gene: tll0569 / Plasmid: pBAD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DLC7

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-VRB / Phycoviolobilin, blue light-absorbing form / 3-[5-[(3-ethyl-4-methyl-5-oxidanylidene-1,2-dihydropyrrol-2-yl)methyl]-2-[[5-[(Z)-(4-ethyl-3-methyl-5-oxidanylidene-pyr rol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid


Mass: 590.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3350, MgCl2, Bistris, NaCl, HEPES

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.3051 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: May 3, 2018
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3051 Å / Relative weight: 1
ReflectionResolution: 1.5→24.41 Å / Num. obs: 51176 / % possible obs: 97.86 % / Redundancy: 174.1 % / CC1/2: 0.969 / Net I/σ(I): 56.3
Reflection shellResolution: 1.5→1.526 Å / Mean I/σ(I) obs: 1.001 / Num. unique obs: 1616 / CC1/2: 0.046

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.04 Å24.41 Å
Translation6.04 Å24.41 Å

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Processing

Software
NameVersionClassification
PHASER2.6.0phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
cctbx.xfeldata reduction
DIALSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified PDBID 4FOF

4fof


Resolution: 1.55→24.086 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.96
RfactorNum. reflection% reflection
Rfree0.1852 2737 5.92 %
Rwork0.1574 --
obs0.1588 46217 97.39 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 154.29 Å2 / Biso mean: 36.879 Å2 / Biso min: 13.14 Å2
Refinement stepCycle: final / Resolution: 1.55→24.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 274 245 2935
Biso mean--34.19 47.97 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.57680.43621450.4055126060
1.5768-1.60540.43241980.3864189090
1.6054-1.63630.37622330.3538205598
1.6363-1.66970.33782010.32932128100
1.6697-1.7060.32511590.28762170100
1.706-1.74570.25081270.25642215100
1.7457-1.78930.24811050.22992265100
1.7893-1.83770.28471370.19582183100
1.8377-1.89170.23751080.19492245100
1.8917-1.95270.22931250.17792244100
1.9527-2.02250.23941100.15762230100
2.0225-2.10340.16761220.14562239100
2.1034-2.19910.17051200.14522240100
2.1991-2.3150.1841170.14412270100
2.315-2.45990.18071260.14982257100
2.4599-2.64960.19131140.15042279100
2.6496-2.91580.17591210.15122265100
2.9158-3.33680.1471130.1392286100
3.3368-4.20040.11551290.12212327100
4.2004-24.0860.15291270.14062432100
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)
12.18050.1176-0.0121.7177-0.13722.7053-0.0637-0.04890.0088-0.02460.03820.0702-0.00930.0158-0.00380.13730.00660.01620.14190.00010.1638-2.94-6.2847.514
21.41370.07710.52952.9221-0.53623.41560.023-0.00090.0433-0.1328-0.0578-0.0494-0.15940.0447-0.00370.1612-0.0332-0.00320.18030.00430.193210.47-11.4136.516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 435:584 OR RESID 601:601 ) )A435 - 584
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 435:584 OR RESID 601:601 ) )A601
3X-RAY DIFFRACTION2( CHAIN B AND ( RESID 435:584 OR RESID 601:601 ) )B435 - 584
4X-RAY DIFFRACTION2( CHAIN B AND ( RESID 435:584 OR RESID 601:601 ) )B601

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