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- PDB-1t1a: Late intermediate IL1 from time-resolved crystallography of the E... -

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Basic information

Entry
Database: PDB / ID: 1t1a
TitleLate intermediate IL1 from time-resolved crystallography of the E46Q mutant of PYP
ComponentsPhotoactive yellow protein
Keywordsphotoreceptor / photoactive yellow protein / PAS domain
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 / Resolution: 1.6 Å
AuthorsRajagopal, S. / Anderson, S. / Srajer, V. / Schmidt, M. / Pahl, R. / Moffat, K.
CitationJournal: Structure / Year: 2005
Title: A Structural Pathway for Signaling in the E46Q Mutant of Photoactive Yellow Protein
Authors: Rajagopal, S. / Anderson, S. / Srajer, V. / Schmidt, M. / Pahl, R. / Moffat, K.
History
DepositionApr 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 9, 2015Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 27, 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

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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
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.917, 66.917, 41.002
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Number of models2

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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) / Gene: PYP / 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 13957

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
LaueViewdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.6→30 Å / Num. parameters: 3949 / Num. restraintsaints: 11002 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.3313 1306 13.4 %RANDOM
Rwork0.313 ---
all0.3147 13889 --
obs0.3147 13889 100 %-
Refine analyzeNum. disordered residues: 125 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 987
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 11 0 987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0263
X-RAY DIFFRACTIONs_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.022
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0

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