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- PDB-1otb: WILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K -

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Basic information

Entry
Database: PDB / ID: 1otb
TitleWILD TYPE PHOTOACTIVE YELLOW PROTEIN, P63 AT 295K
ComponentsPhotoactive yellow protein
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: 1.1 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 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)14,0532
Polymers13,8891
Non-polymers1641
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.833, 66.833, 40.947
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13888.575 Da / Num. of mol.: 1
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.: 113 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, sodium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 295 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: 1.1→100 Å / Num. all: 42402 / Num. obs: 42402 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 17 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.6
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.5 / % possible all: 81.5

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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: 1.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: derived from 1.0A (110K) wild type ground state structure
RfactorNum. reflectionSelection details
Rfree0.161 2048 RANDOM
Rwork0.131 --
all0.133 42402 -
obs0.133 40991 -
Refinement stepCycle: LAST / Resolution: 1.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 113 1100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d2.31

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