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- PDB-6p58: Dark and Steady State-Illuminated Crystal Structure of Cyanobacte... -

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Basic information

Entry
Database: PDB / ID: 6p58
TitleDark and Steady State-Illuminated Crystal Structure of Cyanobacteriochrome Receptor PixJ at 150K
ComponentsMethyl-accepting chemotaxis protein
KeywordsSIGNALING PROTEIN / phytochrome / bilin / light-sensing / temperature-scan
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
Phycoviolobilin, blue light-absorbing form / Methyl-accepting chemotaxis protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.499 Å
AuthorsClinger, J.A. / Miller, M.D. / Buirgie, E.S. / Vierstra, R.D. / Phillips Jr., G.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)STC-1231306 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127892 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
DepositionMay 29, 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _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_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.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

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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)35,70810
Polymers34,3052
Non-polymers1,4038
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-32 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.618, 61.052, 116.148
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DLC7
#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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.5 / Details: 100mM HEPES pH 7.5, 18% w/v PEG 3350, 200mM MgCl2

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9919 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 1.5→33.8 Å / Num. obs: 48186 / % possible obs: 99.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.047 / Rrim(I) all: 0.123 / Net I/σ(I): 8 / Num. measured all: 320193 / Scaling rejects: 348
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
1.5-1.546.81.5452401735570.5780.6411.6761.2100
6.71-33.86.10.03438806350.9990.0140.03726.899.4

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GLQ

4glq


Resolution: 1.499→33.828 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.27
RfactorNum. reflection% reflection
Rfree0.1957 2435 5.06 %
Rwork0.1593 --
obs0.161 48093 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.42 Å2 / Biso mean: 25.9884 Å2 / Biso min: 10.72 Å2
Refinement stepCycle: final / Resolution: 1.499→33.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 186 309 2903
Biso mean--25.28 40.67 -
Num. residues----300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4992-1.52980.3331360.28912570270697
1.5298-1.5630.31021420.265926582800100
1.563-1.59940.27751410.254126582799100
1.5994-1.63940.27891420.225626552797100
1.6394-1.68370.25891410.213526522793100
1.6837-1.73320.22921350.19626592794100
1.7332-1.78920.20611560.187426752831100
1.7892-1.85310.21471400.176626602800100
1.8531-1.92730.2021490.16982658280799
1.9273-2.0150.17371390.14472615275497
2.015-2.12120.17521480.128526862834100
2.1212-2.25410.18311490.128826892838100
2.2541-2.42810.15691470.132227042851100
2.4281-2.67240.17361380.137827162854100
2.6724-3.05880.16961560.137327262882100
3.0588-3.8530.17251410.13592759290099
3.853-33.83680.21371350.174729183053100

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