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- PDB-4hh1: Dark-state structure of AppA wild-type without the Cys-rich regio... -

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Basic information

Entry
Database: PDB / ID: 4hh1
TitleDark-state structure of AppA wild-type 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 / rigid body / Resolution: 3.501 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 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 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)88,6634
Polymers87,7502
Non-polymers9132
Water0
1
A: AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3312
Polymers43,8751
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AppA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3312
Polymers43,8751
Non-polymers4561
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-20 kcal/mol
Surface area34050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.530, 70.530, 383.810
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: 43875.023 Da / Num. of mol.: 2 / Fragment: UNP residues 3-399 / Mutation: 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

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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: 3.14 Å3/Da / Density % sol: 60.83 %
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: May 27, 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: 3.5→58 Å / Num. all: 14286 / Num. obs: 14223 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 84.1 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.9
Reflection shellResolution: 3.5→3.6 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.836 / Mean I/σ(I) obs: 2.45 / Num. unique all: 1111 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: rigid body / Resolution: 3.501→58 Å / SU ML: 0.33 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 20.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2257 705 4.96 %random
Rwork0.186 ---
all0.188 14286 --
obs0.188 14209 99.53 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.7 Å2
Refinement stepCycle: LAST / Resolution: 3.501→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 62 0 5862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085960
X-RAY DIFFRACTIONf_angle_d1.0368104
X-RAY DIFFRACTIONf_dihedral_angle_d12.782188
X-RAY DIFFRACTIONf_chiral_restr0.064961
X-RAY DIFFRACTIONf_plane_restr0.0071045
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5014-3.77170.27591250.24382652X-RAY DIFFRACTION100
3.7717-4.15120.27011390.20872716X-RAY DIFFRACTION100
4.1512-4.75160.20951340.17092656X-RAY DIFFRACTION100
4.7516-5.98560.23071780.18532678X-RAY DIFFRACTION100
5.9856-58.21170.18991290.16342802X-RAY DIFFRACTION99
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)
10.0212-0.0180.0160.0775-0.0310.0561-0.1212-0.10980.04310.1293-0.0389-0.11150.1290.2252-0.01250.73830.1902-0.00040.581-0.04870.414154.398922.8871212.6781
20.03390.0332-0.0470.063-0.01150.09330.23090.15470.0492-0.0198-0.0618-0.0476-0.15920.1923-00.62850.08410.06370.3942-0.05780.409242.617642.7791204.8053
30.04040.01740.06420.03210.01330.13890.15670.00940.19570.05720.0479-0.0087-0.0730.23590.02530.6562-0.27850.15590.554-0.14160.527751.794156.7319219.6573
40.0463-0.0062-0.02180.14080.03620.0247-0.06090.0574-0.0893-0.07550.00770.09560.0292-0.0291-0.18540.6885-0.2635-0.04660.27420.01720.48729.485423.8236.2402
50.03380.0386-0.01080.05830.00390.06920.0897-0.06630.048-0.03150.0048-0.0439-0.0660.01850.12920.7261-0.34840.05590.36390.00770.46821.505444.7368241.3884
60.18770.0908-0.05840.17280.16870.32480.18440.00190.00510.04070.0521-0.0692-0.1165-0.29430.05480.5832-0.07520.14560.25870.0630.353711.557155.5416224.7924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 117)
2X-RAY DIFFRACTION2chain 'A' and (resid 118 through 263)
3X-RAY DIFFRACTION3chain 'A' and (resid 264 through 398 )
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 117 )
5X-RAY DIFFRACTION5chain 'B' and (resid 118 through 263 )
6X-RAY DIFFRACTION6chain 'B' and (resid 264 through 398 )

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