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- PDB-7rha: A new fluorescent protein darkmRuby at pH 5.0 -

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Basic information

Entry
Database: PDB / ID: 7rha
TitleA new fluorescent protein darkmRuby at pH 5.0
ComponentsdarkmRuby
KeywordsFLUORESCENT PROTEIN / Dark fluorescent protein / mRuby
Function / homologyACETATE ION
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuang, M. / Ng, H.L. / Zhang, S. / Deng, M. / Chu, J.
CitationJournal: To Be Published
Title: Crystal structure of a new fluorescent protein darkmRuby at pH 5.0
Authors: Huang, M. / Zhang, S. / Deng, M. / Zou, Y. / Lin, M.Z. / Ng, H.L. / Chu, J.
History
DepositionJul 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: darkmRuby
A: darkmRuby
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,07318
Polymers53,0182
Non-polymers1,05516
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.571, 101.685, 134.983
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein darkmRuby


Mass: 26509.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia phage EcSzw-2 (virus)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M lithium sulfate, 0.1 M sodium acetate: acetic acid pH 4.5, 30% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→47.62 Å / Num. obs: 47367 / % possible obs: 100 % / Redundancy: 7.36 % / CC1/2: 0.997 / Net I/σ(I): 10.4
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 6812 / CC1/2: 0.842 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3u0l

3u0l


Resolution: 1.8→47.58 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.656 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2106 2366 5 %RANDOM
Rwork0.1756 ---
obs0.1773 44943 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.22 Å2 / Biso mean: 22.209 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å20 Å2
2---0.54 Å2-0 Å2
3---1.8 Å2
Refinement stepCycle: final / Resolution: 1.8→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3502 0 66 246 3814
Biso mean--42.65 31.96 -
Num. residues----441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133898
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173658
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6715283
X-RAY DIFFRACTIONr_angle_other_deg1.3261.5838480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1035498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.43721.667210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85715670
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151524
X-RAY DIFFRACTIONr_chiral_restr0.0710.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02890
LS refinement shellResolution: 1.8→1.844 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.312 171 -
Rwork0.31 3251 -
obs--98.87 %

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