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- PDB-6pu2: Dark, Mutant H275T , 100K, PCM Myxobacterial Phytochrome, P2 -

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Basic information

Entry
Database: PDB / ID: 6pu2
TitleDark, Mutant H275T , 100K, PCM Myxobacterial Phytochrome, P2
ComponentsPhotoreceptor-histidine kinase BphP
KeywordsSIGNALING PROTEIN / Dark / Mutant H275T / 100K / PCM Myxobacterial Phytochrome / P2
Function / homology
Function and homology information


detection of visible light / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...: / Phytochrome / Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / 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 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / PAS domain superfamily / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Chem-EL5 / histidine kinase
Similarity search - Component
Biological speciesStigmatella aurantiaca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPandey, S. / Schmidt, M. / Stojkovic, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Struct Dyn. / Year: 2019
Title: High-resolution crystal structures of a myxobacterial phytochrome at cryo and room temperatures.
Authors: Sanchez, J.C. / Carrillo, M. / Pandey, S. / Noda, M. / Aldama, L. / Feliz, D. / Claesson, E. / Wahlgren, W.Y. / Tracy, G. / Duong, P. / Nugent, A.C. / Field, A. / Srajer, V. / Kupitz, C. / ...Authors: Sanchez, J.C. / Carrillo, M. / Pandey, S. / Noda, M. / Aldama, L. / Feliz, D. / Claesson, E. / Wahlgren, W.Y. / Tracy, G. / Duong, P. / Nugent, A.C. / Field, A. / Srajer, V. / Kupitz, C. / Iwata, S. / Nango, E. / Tanaka, R. / Tanaka, T. / Fangjia, L. / Tono, K. / Owada, S. / Westenhoff, S. / Schmidt, M. / Stojkovic, E.A.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 24, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.3Jan 31, 2024Group: Data collection / Structure summary / Category: chem_comp / chem_comp_atom / chem_comp_bond / Item: _chem_comp.pdbx_synonyms
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Photoreceptor-histidine kinase BphP
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8604
Polymers103,6912
Non-polymers1,1692
Water5,477304
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A: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4302
Polymers51,8451
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Photoreceptor-histidine kinase BphP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4302
Polymers51,8451
Non-polymers5851
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.405, 81.790, 83.493
Angle α, β, γ (deg.)90.00, 107.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Photoreceptor-histidine kinase BphP


Mass: 51845.336 Da / Num. of mol.: 2 / Mutation: H275T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stigmatella aurantiaca (strain DW4/3-1) (bacteria)
Strain: DW4/3-1 / Gene: STIAU_8420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09E27
#2: Chemical ChemComp-EL5 / 3-[(2Z)-2-({3-(2-carboxyethyl)-5-[(E)-(4-ethenyl-3-methyl-5-oxo-1,5-dihydro-2H-pyrrol-2-ylidene)methyl]-4-methyl-1H-pyrrol-2-yl}methylidene)-5-{(Z)-[(3E,4S)-3-ethylidene-4-methyl-5-oxopyrrolidin-2-ylidene]methyl}-4-methyl-2H-pyrrol-3-yl]propanoic acid / biliverdin, bound form at Pfr state


Mass: 584.662 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H36N4O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Ammonium acetate, Sodium citrate tribasic dihydrate, PEG 4000, Benzamidine Hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 45897 / % possible obs: 100 % / Redundancy: 2.6 % / Rsym value: 0.092 / Net I/σ(I): 184.5
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 2049 / Rsym value: 0.322

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.24 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2896 --
Rwork0.2191 --
obs-44482 82.66 %
Refinement stepCycle: LAST / Resolution: 2.2→42.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 86 304 7692

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