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- PDB-6pru: Photoconvertible crystals of PixJ from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 6pru
TitlePhotoconvertible crystals of PixJ from Thermosynechococcus elongatus
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.539 Å
Model detailsStructure of photoconvertible TePixJ as Pb
AuthorsBurgie, E.S. / Clinger, J.A. / Miller, M.D. / Phillips Jr., G.N. / Vierstra, R.D.
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 11, 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 2.0Jan 22, 2020Group: Database references / Polymer sequence / Category: citation / entity_poly
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _entity_poly.pdbx_target_identifier
Revision 2.1Oct 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
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_alt_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

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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)36,47926
Polymers34,3052
Non-polymers2,17424
Water5,441302
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A: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,06910
Polymers17,1521
Non-polymers9169
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methyl-accepting chemotaxis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,41016
Polymers17,1521
Non-polymers1,25715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.590, 61.085, 116.297
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 (strain BP-1) (bacteria)
Strain: BP-1 / Gene: tll0569 / Plasmid: pBAD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DLC7

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Non-polymers , 6 types, 326 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.2 Å3/Da / Density % sol: 44.11 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.5 / Details: PEG 3350, MgCl2, Bistris, NaCl, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2018
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 1.539→58.15 Å / Num. obs: 45364 / % possible obs: 98.9 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.024 / Rrim(I) all: 0.087 / Net I/σ(I): 14.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.54-1.628.92.0385432061200.5690.7082.165193.1
4.87-58.15120.0431959316280.9990.0130.04445.6100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.86 Å58.15 Å
Translation2.86 Å58.15 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.3data scaling
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: modified PDBID 4FOF

4fof


Resolution: 1.539→42.117 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.06
RfactorNum. reflection% reflection
Rfree0.2067 2644 5.84 %
Rwork0.163 --
obs0.1653 45272 98.76 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å
Displacement parametersBiso max: 115.51 Å2 / Biso mean: 32.936 Å2 / Biso min: 13.7 Å2
Refinement stepCycle: final / Resolution: 1.539→42.117 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 271 337 3024
Biso mean--43.96 44.26 -
Num. residues----300
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5394-1.56740.36172190.3612188187
1.5674-1.59760.37622150.3415196793
1.5976-1.63020.36842230.3082212198
1.6302-1.66560.341710.273217499
1.6656-1.70440.27621200.24342276100
1.7044-1.7470.2761170.22272243100
1.747-1.79420.25581210.19792269100
1.7942-1.8470.26091170.18852266100
1.847-1.90660.23961190.18052269100
1.9066-1.97480.23041200.15962259100
1.9748-2.05380.17911210.15362282100
2.0538-2.14730.19171150.15482277100
2.1473-2.26050.2081260.14892287100
2.2605-2.40210.16941200.15052281100
2.4021-2.58760.20641220.15272296100
2.5876-2.84790.17391210.14712316100
2.8479-3.25990.19611210.14562336100
3.2599-4.10660.15271250.13522349100
4.1066-42.1170.20141310.16472479100
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)
11.82170.0025-0.2451.95710.11612.31780.0090.00290.0001-0.1754-0.0423-0.00830.1455-0.1464-0.00330.1652-0.02720.05210.167-0.00870.177-2.4554-6.28258.3915
21.067-0.14490.55682.5701-0.29312.9773-0.115-0.04780.0273-0.10510.0474-0.172-0.14690.0069-0.00030.1428-0.0128-0.00250.20140.00190.206810.4301-11.85935.538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 435 through 584)A435 - 584
2X-RAY DIFFRACTION2(chain 'B' and resid 435 through 584)B435 - 584

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