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- PDB-1odv: Photoactive yellow protein 1-25 deletion mutant -

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Basic information

Entry
Database: PDB / ID: 1odv
TitlePhotoactive yellow protein 1-25 deletion mutant
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsSIGNALLING / PHOTOACTIVITY / P-COUMARIC ACID
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 speciesECTOTHIORHODOSPIRA HALOPHILA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsVreede, J. / Van Der horst, M.A. / Hellingwerf, K.J. / Crielaard, W. / Van Aalten, D.M.F.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Pas Domains.Common Structure and Common Flexibility
Authors: Vreede, J. / Van Der Horst, M.A. / Hellingwerf, K.J. / Crielaard, W. / Van Aalten, D.M.F.
History
DepositionMar 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
B: PHOTOACTIVE YELLOW PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6924
Polymers22,3632
Non-polymers3282
Water6,557364
1
A: PHOTOACTIVE YELLOW PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3462
Polymers11,1821
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PHOTOACTIVE YELLOW PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3462
Polymers11,1821
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.566, 82.566, 63.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2106-

HOH

21B-2178-

HOH

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN / PYP


Mass: 11181.659 Da / Num. of mol.: 2 / Fragment: RESIDUES 26-125
Source method: isolated from a genetically manipulated source
Details: P-COUMARIC ACID
Source: (gene. exp.) ECTOTHIORHODOSPIRA 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.: 2 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Compound detailsPHOTOACTIVE BLUE-LIGHT PROTEIN THAT PROBABLY FUNCTIONS AS A PHOTORECEPTOR FOR A NEGATIVE PHOTOTAXIS ...PHOTOACTIVE BLUE-LIGHT PROTEIN THAT PROBABLY FUNCTIONS AS A PHOTORECEPTOR FOR A NEGATIVE PHOTOTAXIS RESPONSE. COVALENTLY BINDS A 4-HYDROXYCINNAMYL (P-COUMARIC ACID) CHOROMOPHORE VIA A THIOESTER LINKAGE.

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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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growpH: 7.5
Details: CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER ...Details: CRYSTALS WERE GROWN BY EQUILIBRATION OF 1 ML OF 30 MG/ML PROTEIN WITH 1 ML OF MOTHER LIQUOR (1.8 M AMMONIUM SULPHATE, 10 MM COCL[2], 100 MM MES PH 6.5) AGAINST A 1 ML RESERVOIR OF MOTHER LIQUOR. CRYSTALS APPEARED AFTER 2-3 DAYS A LARGEST DIMENSION OF 0.4 MM.
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein11
21.8 Mammonium sulfate12
310 mM12CoCl2
4100 mMMES12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorDate: Nov 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.14→17 Å / Num. obs: 299780 / % possible obs: 94.4 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.5
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.3 / % possible all: 89.2
Reflection
*PLUS
Num. obs: 75208 / Num. measured all: 299780
Reflection shell
*PLUS
% possible obs: 89.2 %

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Processing

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

2phy


Resolution: 1.14→17 Å / Num. parameters: 17869 / Num. restraintsaints: 21180 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 1096 0 %RANDOM
all0.1473 74065 --
obs0.1473 -93 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 1459 / Occupancy sum non hydrogen: 1919
Refinement stepCycle: LAST / Resolution: 1.14→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 22 364 1962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0304
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.052
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.032
X-RAY DIFFRACTIONs_approx_iso_adps0.06
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2

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