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- PDB-1ote: E46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K -

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Basic information

Entry
Database: PDB / ID: 1ote
TitleE46Q MUTANT OF PHOTOACTIVE YELLOW PROTEIN, P65 AT 110K
Componentsphotoactive yellow protein, PYP
KeywordsSIGNALING PROTEIN / PYP
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: 1.4 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
Revision 1.6Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: photoactive yellow protein, PYP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0522
Polymers13,8881
Non-polymers1641
Water2,486138
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.018, 40.018, 117.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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) / 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.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. all: 20725 / Num. obs: 20725 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 24.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.3
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 13.2 / % possible all: 94.3

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHY

2phy


Resolution: 1.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: derived from 0.95A 110K E46Q mutant ground state structure
RfactorNum. reflectionSelection details
Rfree0.228 988 RANDOM
Rwork0.182 --
all0.185 20725 -
obs0.185 19844 -
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms949 0 11 138 1098
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.44
X-RAY DIFFRACTIONs_bond_d0.015

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