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- PDB-1ot6: CRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE Y... -

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Basic information

Entry
Database: PDB / ID: 1ot6
TitleCRYOTRAPPED CRYSTAL STRUCTURE OF THE E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN UNDER CONTINUOUS ILLUMINATION AT 110K
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PYP / cryotrapping
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS domain / Beta-Lactamase / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsAnderson, S. / Crosson, S. / Moffat, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Short hydrogen bonds in photoactive yellow protein.
Authors: Anderson, S. / Crosson, S. / Moffat, K.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE Model 1 is associated with the photoactivated state and Model 2 is associated with the ...BIOMOLECULE Model 1 is associated with the photoactivated state and Model 2 is associated with the ground state of the protein.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,8881
Non-polymers1641
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.186, 66.186, 40.504
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Number of models2

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13887.591 Da / Num. of mol.: 1 / Mutation: E46Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: PYP / Production host: Escherichia coli (E. coli) / References: UniProt: P16113
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 1.84 Å3/Da / Density % sol: 33.28 %
Description: Author collected the first dataset in the dark, then a second dataset was collected on the same crystal after inducing a photostationary state with continuous illumination. The structure ...Description: Author collected the first dataset in the dark, then a second dataset was collected on the same crystal after inducing a photostationary state with continuous illumination. The structure was refined by the application of difference refinement to both datasets.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.95→100 Å / Num. all: 63595 / Num. obs: 63595 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 26.5
Reflection shellResolution: 0.95→0.98 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 26.5 / % possible all: 78.5

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.161 2971 RANDOM
Rwork0.143 --
all0.144 63595 -
obs0.144 59350 -
Refinement stepCycle: LAST / Resolution: 0.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 185 1172
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.61
X-RAY DIFFRACTIONs_bond_d0.016

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