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- PDB-2qws: Neutron and X-ray structural studies of short hydrogen bonds in P... -

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Basic information

Entry
Database: PDB / ID: 2qws
TitleNeutron and X-ray structural studies of short hydrogen bonds in Photoactive Yellow Protein (PYP)
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / neutron / hydrogen bond / photocycle / Chromophore / Photoreceptor protein / Receptor / Sensory transduction
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
DEUTERATED WATER / 4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFisher, S.Z. / Langan, P.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)
Authors: Fisher, S.Z. / Anderson, S. / Henning, R. / Moffat, K. / Langan, P. / Thiyagarajan, P. / Schultz, A.J.
History
DepositionAug 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.833, 66.833, 40.947
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
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Strain: BN9626 / Gene: pyp / 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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: D2O

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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: 35.29 %
Crystal growTemperature: 293 K / pH: 7
Details: 2.6 M ammonium sulfate in 50 mM sodium phosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 0.6, 7.0
DetectorType: HE3-FILLED NEUTRON DETECTOR / Detector: AREA DETECTOR / Date: Aug 8, 2006
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.61
271
ReflectionResolution: 2.5→34 Å / Num. obs: 3172 / % possible obs: 88.8 % / Observed criterion σ(I): 3.4 / Redundancy: 3.3 % / Rsym value: 0.312
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.7 % / Rsym value: 0.413 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PCSdata collection
CNSrefinement
nCNSrefinement
d*TREKMODIFIED FOR NEUTRON LAUEdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTB

1otb


Resolution: 2.5→34 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 --RANDOM
Rwork0.262 ---
obs-2650 88.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 11 68 1054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.99
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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