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- PDB-5hdc: Femtosecond Structural Dynamics Drives the Trans/Cis Isomerizatio... -

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Basic information

Entry
Database: PDB / ID: 5hdc
TitleFemtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 100 fs to 400 fs Structure
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PHOTORECEPTOR CIS TRANS ISOMERIZATION / TRANS CIS ISOMERIZATION / FREE ELECTRON LASER
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 / Resolution: 1.6 Å
AuthorsPande, K. / Tenboer, J. / Schmidt, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF-0952643 United States
National Science Foundation (NSF, United States)NSF-1231306 United States
CitationJournal: Science / Year: 2016
Title: Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.
Authors: Pande, K. / Hutchison, C.D. / Groenhof, G. / Aquila, A. / Robinson, J.S. / Tenboer, J. / Basu, S. / Boutet, S. / DePonte, D.P. / Liang, M. / White, T.A. / Zatsepin, N.A. / Yefanov, O. / ...Authors: Pande, K. / Hutchison, C.D. / Groenhof, G. / Aquila, A. / Robinson, J.S. / Tenboer, J. / Basu, S. / Boutet, S. / DePonte, D.P. / Liang, M. / White, T.A. / Zatsepin, N.A. / Yefanov, O. / Morozov, D. / Oberthuer, D. / Gati, C. / Subramanian, G. / James, D. / Zhao, Y. / Koralek, J. / Brayshaw, J. / Kupitz, C. / Conrad, C. / Roy-Chowdhury, S. / Coe, J.D. / Metz, M. / Xavier, P.L. / Grant, T.D. / Koglin, J.E. / Ketawala, G. / Fromme, R. / Srajer, V. / Henning, R. / Spence, J.C. / Ourmazd, A. / Schwander, P. / Weierstall, U. / Frank, M. / Fromme, P. / Barty, A. / Chapman, H.N. / Moffat, K. / van Thor, J.J. / Schmidt, M.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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 / 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: 295 K / Method: liquid diffusion / pH: 7
Details: Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. ...Details: Combine and vortex 4.45M sodium malonate with 100 uL protein (135 mg/ml initial concentration) for a final sodium malonate concentration of 3.2M. Let stand at room temperature for 1 hour. Spin at 10,000g for 2 hours in small spin concentrators. Vortex and let stand at room temperature for 4 hours. Harvest crystals and rebuffer with 3.0M sodium malonate.
PH range: 6.95-7.05 / Temp details: Ambient Room Temperature

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Data collection

DiffractionMean temperature: 295 K
Ambient temp details: Injection of crystals into vacuum. No temperature control.
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.31 Å
DetectorType: CS-PAD CXI-1 / Detector: PIXEL / Date: Mar 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.31 Å / Relative weight: 1
ReflectionResolution: 1.6→19.31 Å / Num. all: 13039 / Num. obs: 13039 / % possible obs: 98.72 % / Redundancy: 300 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
CrystFELdata reduction
CrystFELdata scaling
RefinementResolution: 1.6→19.31 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.719 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25832 655 4.8 %RANDOM
Rwork0.2083 ---
obs0.21068 13039 98.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.462 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 0 92 1079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191044
X-RAY DIFFRACTIONr_bond_other_d0.0020.02969
X-RAY DIFFRACTIONr_angle_refined_deg2.3721.9411409
X-RAY DIFFRACTIONr_angle_other_deg2.5572.9932240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.045124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.6125.81855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.615181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.443153
X-RAY DIFFRACTIONr_chiral_restr0.1320.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021198
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02241
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_it0.4130.526499
X-RAY DIFFRACTIONr_mcbond_other0.4130.526498
X-RAY DIFFRACTIONr_mcangle_it0.7130.787622
X-RAY DIFFRACTIONr_mcangle_other0.7120.786623
X-RAY DIFFRACTIONr_scbond_it0.3130.51545
X-RAY DIFFRACTIONr_scbond_other0.3130.51545
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5090.761787
X-RAY DIFFRACTIONr_long_range_B_refined2.9934.2451222
X-RAY DIFFRACTIONr_long_range_B_other2.6514.1011202
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
Rfree0.368 38 -
Rwork0.305 897 -
obs--93.22 %

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