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- PDB-3ve3: Structure of IT Intermediate from time-resolved laue crystallography -

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Basic information

Entry
Database: PDB / ID: 3ve3
TitleStructure of IT Intermediate from time-resolved laue crystallography
ComponentsPhotoactive yellow protein
KeywordsLUMINESCENT PROTEIN / PHOTORECEPTOR / CHROMOPHORE / SENSORY TRANSDUCTION
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 / AB INITIO PHASING / Resolution: 1.6 Å
AuthorsIhee, H. / Jung, Y.O.
CitationJournal: NAT.CHEM. / Year: 2013
Title: Volume-conserving trans-cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography
Authors: Jung, Y.O. / Lee, J.H. / Kim, J. / Schmidt, M. / Moffat, K. / Srajer, V. / Ihee, H.
History
DepositionJan 7, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.833, 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 / Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / 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
Has protein modificationY
Nonpolymer detailsHC4 IS A CHROMOPHORE OF THIS PROTEIN.

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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: 35.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.6M AMMONIUM SULFATE, 50MM SODIUM PHOSPHATE, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.77-1.24
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 15, 2005
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.771
21.241
ReflectionResolution: 1.6→28.9 Å / Num. obs: 13891

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Processing

Software
NameClassification
LaueViewdata scaling
SHELXL-97refinement
LaueViewdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.6→10 Å / Num. parameters: 3952 / Num. restraintsaints: 4021 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STRUCTURE FACTOR FILE REGARDING TO PDB FILE WAS BACK FOURIER-TRANSFORMED AND WAS EXTRAPOLATED FROM THE TIME-INDEPENDENT DIFFERENCE ELECTRON DENSITY MAP. THIS MAP WAS GENERATED USING ...Details: THE STRUCTURE FACTOR FILE REGARDING TO PDB FILE WAS BACK FOURIER-TRANSFORMED AND WAS EXTRAPOLATED FROM THE TIME-INDEPENDENT DIFFERENCE ELECTRON DENSITY MAP. THIS MAP WAS GENERATED USING KINETIC ANALYSIS BASED ON SEVERAL EXPERIMENTAL TIME-DEPENDENT DIFFERENCE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 637 -RANDOM
all0.247 14622 --
obs0.239 13891 95.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 0 987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0

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