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- PDB-2pr5: Structural Basis for Light-dependent Signaling in the Dimeric LOV... -

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Basic information

Entry
Database: PDB / ID: 2pr5
TitleStructural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Dark Structure)
ComponentsBlue-light photoreceptor
KeywordsFLAVOPROTEIN / SIGNALING PROTEIN / light-oxygen-voltage / LOV / Per-Arnt-Sim / PAS
Function / homology
Function and homology information


response to stimulus / photoreceptor activity
Similarity search - Function
STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain ...STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS-associated, C-terminal / PAC domain profile. / PAS domain / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / Beta-Lactamase / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / FLAVIN MONONUCLEOTIDE / Blue-light photoreceptor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMoglich, A. / Moffat, K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Light-dependent Signaling in the Dimeric LOV Domain of the Photosensor YtvA.
Authors: Moglich, A. / Moffat, K.
History
DepositionMay 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: Blue-light photoreceptor
B: Blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2967
Polymers30,2402
Non-polymers1,0565
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-30 kcal/mol
Surface area14040 Å2
MethodPISA
2
A: Blue-light photoreceptor
B: Blue-light photoreceptor
hetero molecules

A: Blue-light photoreceptor
B: Blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,59114
Polymers60,4804
Non-polymers2,11210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area10680 Å2
ΔGint-88 kcal/mol
Surface area24640 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.846, 91.634, 34.239
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Blue-light photoreceptor


Mass: 15119.942 Da / Num. of mol.: 2 / Fragment: residues 20-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: pfyP / Plasmid: pAM001 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O34627
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na acetate pH 4.6, 18-22 % (w/v) PEG-4000, 75-150 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2006
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.45→15 Å / Num. all: 50453 / Num. obs: 48278 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.056 / Χ2: 1.083 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.475.70.44924720.932199.9
1.47-1.56.80.47925051.0491100
1.5-1.536.90.40224871.0011100
1.53-1.566.90.35424980.9991100
1.56-1.66.90.31924430.9931100
1.6-1.636.90.27725350.9561100
1.63-1.676.90.23424700.9931100
1.67-1.726.80.19125250.9681100
1.72-1.776.80.16324710.9491100
1.77-1.836.80.13224980.981100
1.83-1.896.60.11424871.072198.8
1.89-1.975.80.09420991.276183.3
1.97-2.066.60.06925011.0371100
2.06-2.166.60.05825501.0311100
2.16-2.360.05912851.201151.1
2.3-2.486.60.04825431.0761100
2.48-2.726.50.04725491.2811100
2.72-3.126.30.04325781.5199.8
3.12-3.916.20.03321371.273182.3
3.91-156.30.03126451.27196.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→14.82 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.306 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2458 5.1 %RANDOM
Rwork0.19 ---
all0.192 50453 --
obs0.192 48050 95.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.45→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 71 452 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222234
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9963062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6825277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24426.81116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00315400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.829156
X-RAY DIFFRACTIONr_chiral_restr0.0810.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021702
X-RAY DIFFRACTIONr_nbd_refined0.1980.21099
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.253
X-RAY DIFFRACTIONr_mcbond_it0.5331.51311
X-RAY DIFFRACTIONr_mcangle_it1.00822160
X-RAY DIFFRACTIONr_scbond_it1.66731007
X-RAY DIFFRACTIONr_scangle_it2.7194.5889
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 170 -
Rwork0.236 3478 -
obs-3648 99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.18513.5317-7.932111.48574.336928.41470.32440.59190.4756-0.3385-0.11711.5414-1.5548-1.8249-0.20720.04680.0714-0.03180.12060.04180.067814.186228.1383-0.4736
20.6258-0.0589-0.01591.29780.17880.65980.04270.00080.01090.0054-0.0008-0.0989-0.05870.03-0.0419-0.071500.0005-0.03750.0015-0.078924.404428.683714.5253
38.6157-10.7017-0.1313.54320.27290.05150.00990.02870.0341-0.0723-0.05520.27210.0025-0.03780.04530.01940.0444-0.01440.0124-0.00260.05684.877947.12015.4676
433.7975-43.0264-31.253595.27359.221351.97121.9960.6393-1.0064-0.9374-0.78270.2951-1.8424-1.4863-1.21340.14930.07410.03690.08190.01340.10834.935928.021911.5871
51.762-0.18790.27271.73310.00520.72810.01130.0435-0.11630.02740.01440.09560.0408-0.0133-0.0257-0.07060.00180.0101-0.0328-0.0095-0.016211.353410.9118.9918
62.6641-6.66971.646519.1371-2.91.88520.17480.1301-0.0741-0.6089-0.19180.2622-0.3113-0.09070.01690.10450.0649-0.01340.0260.01470.042-2.06234.0619-1.077
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA21 - 246 - 9
22AA25 - 12510 - 110
33AA126 - 147111 - 132
44BB21 - 246 - 9
55BB25 - 12510 - 110
66BB126 - 146111 - 131

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