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- PDB-1ugu: Crystal structure of PYP E46Q mutant -

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Basic information

Entry
Database: PDB / ID: 1ugu
TitleCrystal structure of PYP E46Q mutant
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTOSYNTHESIS / photorecepter
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: 1.2 Å
AuthorsSugishima, M. / Tanimoto, Y. / Hamada, N. / Tokunaga, F. / Fukuyama, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of photoactive yellow protein (PYP) E46Q mutant at 1.2 A resolution suggests how Glu46 controls the spectroscopic and kinetic characteristics of PYP.
Authors: Sugishima, M. / Tanimoto, N. / Soda, K. / Hamada, N. / Tokunaga, F. / Fukuyama, K.
History
DepositionJun 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,0522
Polymers13,8881
Non-polymers1641
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.352, 40.352, 118.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological unit is monomer

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN / PYP


Mass: 13887.591 Da / Num. of mol.: 1 / Mutation: E46Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Plasmid: pET16b / 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.: 180 / 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: 1.71 Å3/Da / Density % sol: 27.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.65 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 7, 2003
RadiationMonochromator: Si(111) double monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.65 Å / Relative weight: 1
ReflectionResolution: 1.2→35 Å / Num. all: 33512 / Num. obs: 31902 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.037 / Net I/σ(I): 18.1
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 3170 / Rsym value: 0.368 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHY

2phy


Resolution: 1.2→34.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.685 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19113 1699 5.1 %RANDOM
Rwork0.16523 ---
all0.16658 31742 --
obs0.16658 31742 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.293 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 11 180 1157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022998
X-RAY DIFFRACTIONr_bond_other_d00.02860
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9571344
X-RAY DIFFRACTIONr_angle_other_deg0.80632022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9415122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021130
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02208
X-RAY DIFFRACTIONr_nbd_refined0.2870.3226
X-RAY DIFFRACTIONr_nbd_other0.2910.3989
X-RAY DIFFRACTIONr_nbtor_other0.10.5471
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.5207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.34
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.336
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1871.5607
X-RAY DIFFRACTIONr_mcangle_it1.8532974
X-RAY DIFFRACTIONr_scbond_it2.1413391
X-RAY DIFFRACTIONr_scangle_it3.2434.5369
X-RAY DIFFRACTIONr_rigid_bond_restr1.152998
X-RAY DIFFRACTIONr_sphericity_free2.9732180
X-RAY DIFFRACTIONr_sphericity_bonded2.8352977
LS refinement shellResolution: 1.202→1.233 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.272 136
Rwork0.261 2150

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