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- PDB-2pr6: Structural Basis for Light-dependent Signaling in the Dimeric LOV... -

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Basic information

Entry
Database: PDB / ID: 2pr6
TitleStructural Basis for Light-dependent Signaling in the Dimeric LOV Photosensor YtvA (Light Structure)
ComponentsBlue-light photoreceptor
KeywordsFLAVOPROTEIN / SIGNALING PROTEIN / light-oxygen-voltage / LOV / Per-Arnt-Sim / PAS
Function / homology
Function and homology information


photoreceptor activity
Similarity search - Function
: / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS domain / PAS-associated, C-terminal / PAC domain profile. / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) ...: / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / PAS domain / PAS-associated, C-terminal / PAC domain profile. / 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
FLAVIN MONONUCLEOTIDE / Blue-light photoreceptor
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Blue-light photoreceptor
B: Blue-light photoreceptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1534
Polymers30,2402
Non-polymers9132
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area14080 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)62,3058
Polymers60,4804
Non-polymers1,8254
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area9780 Å2
ΔGint-65 kcal/mol
Surface area24930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.295, 91.678, 34.380
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.71 %
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: 1.95→15 Å / Num. all: 21687 / Num. obs: 21669 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.086 / Χ2: 0.973 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.987.60.37110500.859199.8
1.98-2.027.60.35210730.846199.9
2.02-2.067.80.31910620.8511100
2.06-2.17.90.2610500.817199.9
2.1-2.157.80.25610830.8351100
2.15-2.27.80.22710400.8271100
2.2-2.257.90.19210780.8791100
2.25-2.317.80.18510720.8691100
2.31-2.387.90.16610490.8171100
2.38-2.467.80.15310960.8281100
2.46-2.547.80.13510590.8281100
2.54-2.647.70.12210810.8491100
2.64-2.767.70.09810790.8631100
2.76-2.917.60.09110920.9151100
2.91-3.097.40.07110710.9591100
3.09-3.327.20.06310911.1381100
3.32-3.656.90.05611051.401199.8
3.65-4.176.70.05311151.509199.7
4.17-5.226.70.04411241.356199.9
5.22-156.70.04711991.404199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→14.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.849 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1106 5.1 %RANDOM
Rwork0.181 ---
all0.184 21687 --
obs0.184 21614 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.859 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.95→14.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 62 311 2419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222148
X-RAY DIFFRACTIONr_angle_refined_deg1.4912.0012922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0325251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72426.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44415381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.042156
X-RAY DIFFRACTIONr_chiral_restr0.1090.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021606
X-RAY DIFFRACTIONr_nbd_refined0.2250.21039
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21495
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.219
X-RAY DIFFRACTIONr_mcbond_it0.8541.51310
X-RAY DIFFRACTIONr_mcangle_it1.25622065
X-RAY DIFFRACTIONr_scbond_it2.1931018
X-RAY DIFFRACTIONr_scangle_it3.2714.5857
LS refinement shellResolution: 1.95→1.994 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 57 -
Rwork0.176 1434 -
obs-1491 96.5 %
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)
16.6357-9.5979-9.124922.399516.769714.04540.17811.05-0.3251-1.1973-0.64922.2568-0.4663-1.30860.47110.08030.0195-0.05360.10590.08110.202613.063530.1948-0.1273
20.85470.2923-0.10121.6626-0.1151.34890.04230.0313-0.0161-0.0212-0.0129-0.0667-0.0417-0.0126-0.0294-0.0992-0.00530.0041-0.080.0013-0.097824.601928.968514.5327
316.2849-18.7814-1.944422.81122.89690.60440.18820.0512-0.103-0.292-0.2720.6729-0.2162-0.120.08380.09940.0837-0.03830.08160.0130.08674.904147.28795.4395
439.5086-26.31868.259457.212126.328137.2528-1.0245-1.42632.24311.84630.17990.6203-1.085-1.70420.84460.26220.06540.0780.1342-0.00470.36693.378829.104412.0988
52.9252-0.8622-0.19712.44320.00161.39060.03160.16940.0091-0.0966-0.0375-0.11650.0519-0.05470.0059-0.0731-0.00210.0111-0.058-0.011-0.078611.344810.97899.2021
64.546-11.74250.037536.6645-1.86830.49571.24280.5448-0.0781-2.813-1.03350.5301-0.4247-0.0543-0.20930.45960.1691-0.01350.2447-0.01840.1151-2.023532.6517-0.569
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA20 - 245 - 9
22AA25 - 12510 - 110
33AA126 - 147111 - 132
44BB20 - 245 - 9
55BB25 - 12510 - 110
66BB126 - 144111 - 129

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