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- PDB-3kct: CRYSTAL STRUCTURE OF PAmCherry1 in the photoactivated state -

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Basic information

Entry
Database: PDB / ID: 3kct
TitleCRYSTAL STRUCTURE OF PAmCherry1 in the photoactivated state
ComponentsPAmCherry1 protein
KeywordsFLUORESCENT PROTEIN / photoconversion / chromophore structure / PALM
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesDiscosoma sp. (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMalashkevich, V.N. / Subach, F.V. / Zencheck, W.D. / Xiao, H. / Filonov, G.S. / Almo, S.C. / Verkhusha, V.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Photoactivation mechanism of PAmCherry based on crystal structures of the protein in the dark and fluorescent states.
Authors: Subach, F.V. / Malashkevich, V.N. / Zencheck, W.D. / Xiao, H. / Filonov, G.S. / Almo, S.C. / Verkhusha, V.V.
History
DepositionOct 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PAmCherry1 protein


Theoretical massNumber of molelcules
Total (without water)26,7831
Polymers26,7831
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.866, 84.042, 98.172
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

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Components

#1: Protein PAmCherry1 protein


Mass: 26783.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Gene: PAmCherry / Plasmid: pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: D1MPT3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 66 NRQ IS CHROMOPHORE DERIVED FROM MET, TYR, GLY

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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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1 M Tris HCl, 0.2 M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2009
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 31288 / % possible obs: 90.3 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.089 / Χ2: 2.692 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.713.70.48415471.368145.3
1.71-1.783.80.4523121.656167.6
1.78-1.864.50.4630871.857190.2
1.86-1.965.40.38233982.207199.1
1.96-2.086.40.29434332.251100
2.08-2.246.80.23734452.3641100
2.24-2.466.80.18534632.6351100
2.46-2.826.70.12534793.0141100
2.82-3.556.50.0835033.7111100
3.55-506.60.05636213.592199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.831 / SU B: 4.758 / SU ML: 0.071 / SU R Cruickshank DPI: 0.093 / SU Rfree: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1568 5 %RANDOM
Rwork0.177 ---
obs0.179 31242 90.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.56 Å2 / Biso mean: 27.893 Å2 / Biso min: 15.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1735 0 0 247 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221788
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9852410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.68524.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87215313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.854159
X-RAY DIFFRACTIONr_chiral_restr0.1470.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211371
X-RAY DIFFRACTIONr_mcbond_it1.6443.51061
X-RAY DIFFRACTIONr_mcangle_it4.707501712
X-RAY DIFFRACTIONr_scbond_it8.99750727
X-RAY DIFFRACTIONr_scangle_it2.5474.5696
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 49 -
Rwork0.357 1022 -
all-1071 -
obs--42.62 %
Refinement TLS params.Method: refined / Origin x: -16.9687 Å / Origin y: -27.7725 Å / Origin z: -16.3972 Å
111213212223313233
T0.0144 Å20.0013 Å20.0051 Å2-0.0254 Å20.0071 Å2--0.0067 Å2
L0.3994 °20.2142 °2-0.0399 °2-1.0208 °2-0.3557 °2--0.8058 °2
S0.0123 Å °0.0051 Å °0.0079 Å °-0.079 Å °-0.0406 Å °-0.0326 Å °-0.0242 Å °0.0678 Å °0.0283 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 222
2X-RAY DIFFRACTION1A68 - 477

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