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- PDB-1otd: STRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROL... -

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Basic information

Entry
Database: PDB / ID: 1otd
TitleSTRONG HYDROGEN BONDS IN PHOTOACTIVE YELLOW PROTEIN AND THEIR ROLE IN ITS PHOTOCYCLE
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / PYP
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 / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsAnderson, S. / Crosson, S. / Moffat, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Short hydrogen bonds in photoactive yellow protein.
Authors: Anderson, S. / Crosson, S. / Moffat, K.
History
DepositionMar 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 16, 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_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_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQRES Author states the sequence from the PYP was cloned from the strain SL-1 of ...SEQRES Author states the sequence from the PYP was cloned from the strain SL-1 of Ectothiorhodospira halophila, and there was no appropriate sequence database reference available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoactive yellow protein
B: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4306
Polymers27,7732
Non-polymers6574
Water4,035224
1
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2153
Polymers13,8871
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2153
Polymers13,8871
Non-polymers3282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.983, 91.102, 36.756
Angle α, β, γ (deg.)90.00, 92.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13886.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: PYP / Production host: Escherichia coli (E. coli) / Strain (production host): SL-1 / References: UniProt: P16113
#2: Chemical
ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9.5
Details: PEG 4000, MgCl2, Tris, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 110K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→100 Å / Num. all: 61494 / Num. obs: 61494 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.3
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 56.9

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PHY

2phy


Resolution: 1.25→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: derived from 1.0A (110K) wild type ground state structure
RfactorNum. reflectionSelection details
Rfree0.215 2777 RANDOM
Rwork0.167 --
all0.171 61494 -
obs0.171 55363 -
Refinement stepCycle: LAST / Resolution: 1.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 44 224 1908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d2.61

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