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- PDB-4hh0: Dark-state structure of AppA C20S without the Cys-rich region fro... -

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Basic information

Entry
Database: PDB / ID: 4hh0
TitleDark-state structure of AppA C20S without the Cys-rich region from Rb. sphaeroides
ComponentsAppA protein
KeywordsFLAVOPROTEIN / SIGNALING PROTEIN / BLUF domain / SCHIC domain / photoreceptor / PpsR
Function / homology
Function and homology information


blue light photoreceptor activity / FAD binding
Similarity search - Function
Methionine synthase domain / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Cobalamin-binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 ...Methionine synthase domain / Sensors of blue-light using FAD / BLUF domain profile. / BLUF domain / Sensors of blue-light using FAD / Cobalamin-binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / AppA protein
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / native data for SAD phase extension / Resolution: 2.6 Å
AuthorsWinkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R. / Schlichting, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A ternary AppA-PpsR-DNA complex mediates light regulation of photosynthesis-related gene expression.
Authors: Winkler, A. / Heintz, U. / Lindner, R. / Reinstein, J. / Shoeman, R.L. / Schlichting, I.
History
DepositionOct 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Feb 28, 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: AppA protein
B: AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,26922
Polymers87,7182
Non-polymers1,55120
Water1,44180
1
A: AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,67012
Polymers43,8591
Non-polymers81111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,59910
Polymers43,8591
Non-polymers7409
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-215 kcal/mol
Surface area33590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.260, 70.260, 382.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein AppA protein


Mass: 43858.957 Da / Num. of mol.: 2 / Fragment: UNP residues 3-399 / Mutation: C20S, C399S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.1 / Gene: appA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q53119
#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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.3M tris chloride buffer, 1.3M sodium chloride, 0.3M magnesium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2011 / Details: Dynamically bendable mirror
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48 Å / Num. all: 33951 / Num. obs: 33847 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 67.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 18.2
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.63 / Num. unique all: 3598 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX-AutoSolmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIX-AutoSolphasing
RefinementMethod to determine structure: native data for SAD phase extension
Resolution: 2.6→47.601 Å / SU ML: 0.3 / Isotropic thermal model: isotropic / σ(F): 0 / Phase error: 23.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1715 5.07 %random
Rwork0.1849 ---
all0.187 33951 --
obs0.187 33844 99.71 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 80 80 5960
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055960
X-RAY DIFFRACTIONf_angle_d0.878104
X-RAY DIFFRACTIONf_dihedral_angle_d12.7732188
X-RAY DIFFRACTIONf_chiral_restr0.056961
X-RAY DIFFRACTIONf_plane_restr0.0041045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.69290.27031580.24083199X-RAY DIFFRACTION100
2.6929-2.80070.27861620.24793143X-RAY DIFFRACTION100
2.8007-2.92820.29031750.24863219X-RAY DIFFRACTION100
2.9282-3.08250.30941720.25123150X-RAY DIFFRACTION100
3.0825-3.27560.28711790.23573164X-RAY DIFFRACTION100
3.2756-3.52850.25271820.19843221X-RAY DIFFRACTION100
3.5285-3.88340.21441600.18163220X-RAY DIFFRACTION100
3.8834-4.4450.23641620.16343232X-RAY DIFFRACTION100
4.445-5.59880.19841970.15753197X-RAY DIFFRACTION99
5.5988-47.60910.18371680.16713384X-RAY DIFFRACTION100
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)
15.8982.61050.92267.29760.57565.21920.0123-0.3029-0.07080.7805-0.0045-0.13250.55550.55540.0060.72110.2164-0.00380.52970.00790.382654.320223.0267211.7907
24.1333-3.0311-3.34054.76842.89884.41020.39940.28390.2857-0.3-0.2054-0.1714-0.32470.0782-0.1410.62490.0078-0.02180.38520.00920.329542.478542.7519203.9098
37.11781.01921.09915.39821.26334.30320.146-0.06930.97280.1022-0.0871-0.4192-0.71190.89-0.06880.7408-0.2110.12640.5057-0.0720.632251.582156.6928218.7072
46.29471.6778-0.04687.68991.60463.9236-0.09870.4143-0.4539-0.9290.22630.34930.5141-0.3202-0.0530.9735-0.2924-0.09830.39550.01850.58339.067724.0085235.1534
52.57572.0978-2.05243.4384-1.97383.26280.4049-0.40880.23860.3025-0.29720.1354-0.32010.134-0.05440.8172-0.2491-0.00080.3979-0.01250.508721.35544.8429240.2534
68.3046-1.79110.18265.0538-2.12335.95730.43040.19750.38030.0444-0.03260.4685-0.4584-1.0922-0.28850.6715-0.05970.10460.44760.05460.500211.292155.4753223.6542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 14:117)
2X-RAY DIFFRACTION2chain 'A' and (resseq 118:263)
3X-RAY DIFFRACTION3chain 'A' and (resseq 264:398)
4X-RAY DIFFRACTION4chain 'B' and (resseq 15:118)
5X-RAY DIFFRACTION5chain 'B' and (resseq 119:263)
6X-RAY DIFFRACTION6chain 'B' and (resseq 264:398)

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