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- PDB-2pyr: PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K) -

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Basic information

Entry
Database: PDB / ID: 2pyr
TitlePHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K)
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS
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 / Resolution: 1.9 Å
AuthorsPerman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. ...Perman, B. / Srajer, V. / Ren, Z. / Teng, T.Y. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K.
Citation
Journal: Science / Year: 1998
Title: Energy transduction on the nanosecond time scale: early structural events in a xanthopsin photocycle.
Authors: Perman, B. / Srajer, V. / Ren, Z. / Teng, T. / Pradervand, C. / Ursby, T. / Bourgeois, D. / Schotte, F. / Wulff, M. / Kort, R. / Hellingwerf, K. / Moffat, K.
#1: Journal: Biochemistry / Year: 1995
Title: 1.4 A Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore
Authors: Borgstahl, G.E. / Williams, D.R. / Getzoff, E.D.
History
DepositionMar 4, 1998Processing site: BNL
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _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
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 genetically manipulated source
Details: THIOESTER LINK BETWEEN SG CYS 69 AND C1 HC4 150 / Source: (gene. exp.) Halorhodospira halophila (bacteria) / Strain: BN9626
Description: 4-HYDROXY CINNAMIC ANHYDRIDE CHROMOPHORE RECONSTITUTION
Gene: P16113 / Plasmid: M15-PHISP / 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.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 35.17 % / Description: INITIAL PHASES ARE FROM 2PHY
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
22.5 Mammonium sulfate1drop
320 mMsodium phosphate1drop
42.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.3
DetectorType: THOMPSON / Detector: CCD AREA DETECTOR / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthWavelength: 0.3 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 13027 / % possible obs: 83.4 % / Redundancy: 14 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.5→1.57 Å / Redundancy: 14 % / % possible all: 44.8
Reflection shell
*PLUS
% possible obs: 44.8 %

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Processing

Software
NameClassification
X-PLORmodel building
XTALVIEWrefinement
X-PLORrefinement
LaueViewdata reduction
LaueViewdata scaling
X-PLORphasing
RefinementResolution: 1.9→20 Å / % reflection Rfree: 10 % / Cross valid method: FREE-R
Details: TERWILLIGER/BERENDZEN DIFFERENCE REFINEMENT G RESIDUE IS DARK STRUCTURE, PG R RESIDE IS 1 NANOSECOND STRUCTURE, [PR]. ONLY DIFFERENT CONFORMATIONS AFTER 1 NANOSECOND INCLUDED.
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 92 1068
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rfree: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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