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- PDB-1yrx: Structure of a novel photoreceptor: the BLUF domain of AppA from ... -

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Basic information

Entry
Database: PDB / ID: 1yrx
TitleStructure of a novel photoreceptor: the BLUF domain of AppA from Rhodobacter sphaeroides
Componentshypothetical protein Rsph03001874Hypothesis
KeywordsTRANSCRIPTION / ferredoxin-like fold / flavin binding / photoreceptor
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding
Similarity search - Function
Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Methionine synthase domain / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-DODECYL-N,N-DIMETHYLGLYCINATE / FLAVIN MONONUCLEOTIDE / AppA protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsAnderson, S. / Dragnea, V. / Masuda, S. / Ybe, J. / Moffat, K. / Bauer, C.
CitationJournal: Biochemistry / Year: 2005
Title: Structure of a Novel Photoreceptor, the BLUF Domain of AppA from Rhodobacter sphaeroides
Authors: Anderson, S. / Dragnea, V. / Masuda, S. / Ybe, J. / Moffat, K. / Bauer, C.
History
DepositionFeb 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: hypothetical protein Rsph03001874
B: hypothetical protein Rsph03001874
C: hypothetical protein Rsph03001874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,62512
Polymers40,6273
Non-polymers2,9989
Water1,74797
1
A: hypothetical protein Rsph03001874
B: hypothetical protein Rsph03001874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8127
Polymers27,0852
Non-polymers1,7275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: hypothetical protein Rsph03001874
hetero molecules

C: hypothetical protein Rsph03001874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,62610
Polymers27,0852
Non-polymers2,5418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
3
C: hypothetical protein Rsph03001874
hetero molecules

C: hypothetical protein Rsph03001874
hetero molecules

A: hypothetical protein Rsph03001874
B: hypothetical protein Rsph03001874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,43817
Polymers54,1704
Non-polymers4,26813
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_554-x,-y,z-1/21
crystal symmetry operation7_555y,x,-z1
identity operation1_555x,y,z1
Buried area25720 Å2
ΔGint-137 kcal/mol
Surface area30900 Å2
MethodPISA
4
A: hypothetical protein Rsph03001874
B: hypothetical protein Rsph03001874
C: hypothetical protein Rsph03001874
hetero molecules

A: hypothetical protein Rsph03001874
B: hypothetical protein Rsph03001874
C: hypothetical protein Rsph03001874
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,25024
Polymers81,2556
Non-polymers5,99518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)98.671, 98.671, 127.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological unit is a homodimer, A+B chains form one homodimer and the C chain half of a homodimer

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Components

#1: Protein hypothetical protein Rsph03001874 / Hypothesis / AppA BLUF domain


Mass: 13542.438 Da / Num. of mol.: 3 / Fragment: sequence database residues 17-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Species: Rhodobacter sphaeroides / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53119
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-D9G / N-DODECYL-N,N-DIMETHYLGLYCINATE


Mass: 271.439 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H33NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG3350, ethyleneglycol, tris, DDMG, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9, 0.97939, 0.97962, 0.96113
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979391
30.979621
40.961131
ReflectionResolution: 2.3→50 Å / Num. all: 28629 / Num. obs: 27558 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 24 / Redundancy: 13.7 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.6 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
XTALVIEWrefinement
REFMAC5.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.3→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.273 1378 random
Rwork0.241 --
all0.243 27558 -
obs0.243 25947 -
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 169 97 2962

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