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- PDB-3ume: Structure of pB intermediate of Photoactive yellow protein (PYP) ... -

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Basic information

Entry
Database: PDB / ID: 3ume
TitleStructure of pB intermediate of Photoactive yellow protein (PYP) at pH 7
ComponentsPhotoactive yellow protein
KeywordsPROTEIN BINDING / Photoreceptor
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: 1.8 Å
AuthorsTripathi, S. / Srajer, V. / Purwar, N. / Henning, R. / Schmidt, M.
CitationJournal: Biophys.J. / Year: 2012
Title: pH Dependence of the Photoactive Yellow Protein Photocycle Investigated by Time-Resolved Crystallography.
Authors: Tripathi, S. / Srajer, V. / Purwar, N. / Henning, R. / Schmidt, M.
History
DepositionNov 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 1.2Sep 13, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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

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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
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.900, 66.900, 40.800
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 natural source / Source: (natural) Halorhodospira halophila (bacteria) / 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.: 88 / 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: 35.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.0 M Ammonium Sulfate, 50 mM Sodium Phosphate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.0 - 1.2
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.21
ReflectionResolution: 1.6→30 Å / Num. all: 10000 / Num. obs: 10000 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
XFITdata reduction
CNS1.1refinement
Precognitiondata reduction
Epinormdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2PHY

2phy


Resolution: 1.8→30 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.146 473 Random
Rwork0.1202 --
obs0.146 10000 -
all-10000 -
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 11 88 1074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.48483
X-RAY DIFFRACTIONc_bond_d0.005345
LS refinement shellResolution: 1.8→1.86 Å
RfactorNum. reflection% reflection
Rfree0.254 39 -
Rwork0.1718 --
obs-951 100 %

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