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- PDB-3pyp: PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE -

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Basic information

Entry
Database: PDB / ID: 3pyp
TitlePHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLE INTERMEDIATE
ComponentsPHOTOACTIVE YELLOW PROTEIN
KeywordsPHOTORECEPTOR / LIGHT SENSOR FOR NEGATIVE PHOTOTAXIS
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 / SAME CRYSTAL LATTICE MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsGenick, U.K. / Soltis, S.M. / Kuhn, P. / Canestrelli, I.L. / Getzoff, E.D.
CitationJournal: Nature / Year: 1998
Title: Structure at 0.85 A resolution of an early protein photocycle intermediate.
Authors: Genick, U.K. / Soltis, S.M. / Kuhn, P. / Canestrelli, I.L. / Getzoff, E.D.
History
DepositionJul 28, 1998Processing site: BNL
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)14,0532
Polymers13,8891
Non-polymers1641
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.224, 66.224, 40.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-3001-

HOH

31A-3002-

HOH

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Components

#1: Protein PHOTOACTIVE YELLOW PROTEIN / PYP


Mass: 13888.575 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: THIOESTER LINKAGE BETWEEN THE SULFUR OF CYS 69 AND CARBOXY GROUP OF THE 4-HYDROXY CINNAMIC ACID CHROMOPHORE
Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9626 / 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.: 137 / 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: 1.8 Å3/Da / Density % sol: 32 % / Description: CRYSTALS IDENTICAL TO 2PHY
Crystal growpH: 4.8 / Details: pH 4.8
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: used as seeds
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.2 Mammonium sulfate1reservoir
220 mMsodium phosphate1reservoir
315 mg/mlprotein1drop
42.5 Mammonium sulfate1drop
520 mMsodium phosphate1drop

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Data collection

DiffractionMean temperature: 149 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.77
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 6, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionHighest resolution: 0.85 Å / Num. obs: 84934 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 10.9
Reflection shellResolution: 0.85→0.86 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.52 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 561693
Reflection shell
*PLUS
% possible obs: 87.1 %

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Processing

Software
NameClassification
SHELX-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAME CRYSTAL LATTICE MOLECULAR REPLACEMENT
Starting model: 2PHY

2phy


Resolution: 0.85→50 Å / Num. parameters: 11379 / Num. restraintsaints: 15920 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NUMBER OF PROTEIN AND SOLVENT ATOMS CONTAINS DUAL CONFORMERS
RfactorNum. reflection% reflectionSelection details
Rfree0.1548 4249 5 %5% RANDOMLY CHOSEN BY SHELX
obs0.1326 -97.7 %-
all-80680 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 943 / Occupancy sum non hydrogen: 1133
Refinement stepCycle: LAST / Resolution: 0.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1094 0 11 196 1301
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.112
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.064
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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