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- PDB-2iyi: structure of a light-induced intermediate of the BLUF domain of t... -

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Basic information

Entry
Database: PDB / ID: 2iyi
Titlestructure of a light-induced intermediate of the BLUF domain of the rhodobacterial protein AppA
ComponentsAPPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
KeywordsSIGNAL TRANSDUCTION / BLUF
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / FLAVIN MONONUCLEOTIDE / AppA, antirepressor of ppsR, sensor of blue light
Similarity search - Component
Biological speciesRHODOBACTER SPHAEROIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsJung, A. / Reinstein, J. / Domratcheva, T. / Shoeman, R.-L. / Schlichting, I.
CitationJournal: J. Mol. Biol. / Year: 2006
Title: Crystal structures of the AppA BLUF domain photoreceptor provide insights into blue light-mediated signal transduction.
Authors: Jung, A. / Reinstein, J. / Domratcheva, T. / Shoeman, R.L. / Schlichting, I.
History
DepositionJul 17, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
B: APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0616
Polymers27,8392
Non-polymers1,2214
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.400, 126.400, 64.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT


Mass: 13919.674 Da / Num. of mol.: 2 / Fragment: BLUF DOMAIN, RESIDUES 1-124 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHODOBACTER SPHAEROIDES (bacteria) / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3J677
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Dithioerythritol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 20 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 20 TO SER

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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: 2.96 Å3/Da / Density % sol: 58.09 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.080797
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.080797 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 6700 / % possible obs: 100 % / Observed criterion σ(I): 4.5 / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→19.86 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 31.133 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 335 5 %RANDOM
Rwork0.188 ---
obs0.19 6362 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.97 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.96 Å20 Å2
2--1.93 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 78 48 1807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211795
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9912432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21622.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.65315287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6921520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021342
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21188
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5341.51081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.93321689
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7783865
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6354.5743
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.02 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.424 24
Rwork0.3 452
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)
14.647-2.0671-0.50312.9056-0.38774.391-0.1291-0.01680.09250.2466-0.00760.22530.08-0.55260.1367-0.1937-0.1112-0.0381-0.0827-0.0392-0.11596.435635.9954-0.5142
22.2239-0.84010.39116.1387-1.04635.5555-0.0704-0.21620.1210.6958-0.0832-0.3175-0.11930.25140.1537-0.1904-0.0498-0.1031-0.1714-0.0276-0.130623.518742.86085.0863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 121
2X-RAY DIFFRACTION2B15 - 120

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