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- PDB-6p4i: Photoactive Yellow Protein PYP 10ps -

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Basic information

Entry
Database: PDB / ID: 6p4i
TitlePhotoactive Yellow Protein PYP 10ps
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PYP / 10ps
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
Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPandey, S. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Nat.Methods / Year: 2020
Title: Time-resolved serial femtosecond crystallography at the European XFEL.
Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / ...Authors: Pandey, S. / Bean, R. / Sato, T. / Poudyal, I. / Bielecki, J. / Cruz Villarreal, J. / Yefanov, O. / Mariani, V. / White, T.A. / Kupitz, C. / Hunter, M. / Abdellatif, M.H. / Bajt, S. / Bondar, V. / Echelmeier, A. / Doppler, D. / Emons, M. / Frank, M. / Fromme, R. / Gevorkov, Y. / Giovanetti, G. / Jiang, M. / Kim, D. / Kim, Y. / Kirkwood, H. / Klimovskaia, A. / Knoska, J. / Koua, F.H.M. / Letrun, R. / Lisova, S. / Maia, L. / Mazalova, V. / Meza, D. / Michelat, T. / Ourmazd, A. / Palmer, G. / Ramilli, M. / Schubert, R. / Schwander, P. / Silenzi, A. / Sztuk-Dambietz, J. / Tolstikova, A. / Chapman, H.N. / Ros, A. / Barty, A. / Fromme, P. / Mancuso, A.P. / Schmidt, M.
History
DepositionMay 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Sep 22, 2021Group: Data collection / Database references / Category: database_2 / reflns_shell
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_related_exp_data_set / pdbx_struct_assembly / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.6Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoactive yellow protein


Theoretical massNumber of molelcules
Total (without water)14,0351
Polymers14,0351
Non-polymers00
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: 14034.718 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 7 / Details: Sodium Malonate

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: European XFEL / Beamline: SPB/SFX / Wavelength: 1.3 Å
DetectorType: AGIPD / Detector: PIXEL / Date: Mar 7, 2019
RadiationMonochromator: European XFEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.6→11.15 Å / Num. obs: 12253 / % possible obs: 92.76 % / Redundancy: 284.4 % / Net I/σ(I): 11.77
Reflection shellResolution: 1.6→1.64 Å / Num. unique obs: 685

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WL9

4wl9


Resolution: 1.6→11.15 Å / Cor.coef. Fo:Fc: 0.844 / Cor.coef. Fo:Fc free: 0.776 / SU B: 4.924 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.172 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3415 613 4.8 %RANDOM
Rwork0.28335 ---
obs0.28612 12253 92.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 3.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.6→11.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 92 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021044
X-RAY DIFFRACTIONr_bond_other_d0.0010.02967
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.9621410
X-RAY DIFFRACTIONr_angle_other_deg1.04332237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021198
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2150.336499
X-RAY DIFFRACTIONr_mcbond_other0.2150.336498
X-RAY DIFFRACTIONr_mcangle_it0.3740.503622
X-RAY DIFFRACTIONr_mcangle_other0.3740.502623
X-RAY DIFFRACTIONr_scbond_it0.1130.319545
X-RAY DIFFRACTIONr_scbond_other0.1130.319545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.1930.478788
X-RAY DIFFRACTIONr_long_range_B_refined1.1553.13926
X-RAY DIFFRACTIONr_long_range_B_other0.8683.125906
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 29 -
Rwork0.37 685 -
obs--71.83 %

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