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- PDB-2iyg: Dark state structure of the BLUF domain of the rhodobacterial pro... -

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Basic information

Entry
Database: PDB / ID: 2iyg
TitleDark state structure of the BLUF domain of the rhodobacterial protein AppA
ComponentsAPPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
KeywordsSIGNAL TRANSDUCTION
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding
Similarity search - Function
: / : / AppA, four helix bundle / AppA, sensor containing heme instead of cobalamin / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Sensors of blue-light using FAD / Methionine synthase domain / Acylphosphatase-like domain superfamily ...: / : / AppA, four helix bundle / AppA, sensor containing heme instead of cobalamin / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / 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: 2.3 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: Refinement description / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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
Water1,08160
1
A: APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
B: APPA, ANTIREPRESSOR OF PPSR, SENSOR OF BLUE LIGHT
hetero molecules

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)58,12112
Polymers55,6794
Non-polymers2,4428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area10810 Å2
ΔGint-67.2 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.710, 127.710, 65.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-2028-

HOH

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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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3J677
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


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


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


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


Mass: 18.015 Da / Num. of mol.: 60 / 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
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: 2.99 Å3/Da / Density % sol: 58.5 %
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: 0.92524
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92524 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 17447 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2.3→9.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.156 / SU ML: 0.15 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.268 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.233 707 5 %RANDOM
Rwork0.208 ---
obs0.209 13428 100 %-
Displacement parametersBiso mean: 22.96 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.3→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1700 0 78 60 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9922462
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3595215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28922.55886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.98615291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2351520
X-RAY DIFFRACTIONr_chiral_restr0.0980.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021358
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2768
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7551.51116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19721713
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0163871
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2154.5749
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: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 49
Rwork0.238 944
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)
16.3191-2.4058-0.96573.441-0.83585.2756-0.18630.11330.06340.13630.07060.09080.1896-0.74710.1158-0.2081-0.1117-0.0348-0.0567-0.0057-0.15296.432336.2911-0.3862
22.7626-0.59970.18655.5848-0.91036.6061-0.0062-0.23960.09270.4164-0.0457-0.214-0.06690.37260.0518-0.2291-0.0357-0.0701-0.1993-0.0449-0.146624.007843.04555.163
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 121
2X-RAY DIFFRACTION2B14 - 121

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