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- PDB-3u0m: Crystal structure of the engineered fluorescent protein mRuby, cr... -

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Basic information

Entry
Database: PDB / ID: 3u0m
TitleCrystal structure of the engineered fluorescent protein mRuby, crystal form 1, pH 8.5
ComponentsmRuby
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Red fluorescent protein eqFP611
Function and homology information
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAkerboom, J. / Looger, L.L. / Schreiter, E.R.
CitationJournal: Front Mol Neurosci / Year: 2013
Title: Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics.
Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / ...Authors: Akerboom, J. / Carreras Calderon, N. / Tian, L. / Wabnig, S. / Prigge, M. / Tolo, J. / Gordus, A. / Orger, M.B. / Severi, K.E. / Macklin, J.J. / Patel, R. / Pulver, S.R. / Wardill, T.J. / Fischer, E. / Schuler, C. / Chen, T.W. / Sarkisyan, K.S. / Marvin, J.S. / Bargmann, C.I. / Kim, D.S. / Kugler, S. / Lagnado, L. / Hegemann, P. / Gottschalk, A. / Schreiter, E.R. / Looger, L.L.
History
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Dec 6, 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
A: mRuby


Theoretical massNumber of molelcules
Total (without water)25,8071
Polymers25,8071
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.706, 67.081, 95.001
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mRuby / GFP-like chromoprotein


Mass: 25807.447 Da / Num. of mol.: 1 / Mutation: D196S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ISF8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMRUBY IS THE ENGINEERED VARIANT OF THE RED FLUORESCENT PROTEIN EQFP611

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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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 2, 2010
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→28.66 Å / Num. all: 25160 / Num. obs: 24632 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.74 Å / % possible all: 96.9

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Processing

Software
NameVersionClassification
SPECdata collection
PHASERphasing
REFMAC5.6.0111refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1UIS

1uis


Resolution: 1.65→27.44 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.841 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20074 1256 5.1 %RANDOM
Rwork0.17232 ---
all0.17386 23892 --
obs0.17386 23328 97.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å20 Å2
2---1 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 146 1864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0221882
X-RAY DIFFRACTIONr_bond_other_d0.0010.021315
X-RAY DIFFRACTIONr_angle_refined_deg2.3491.9622560
X-RAY DIFFRACTIONr_angle_other_deg1.08633218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.77823.8184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94215339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8691511
X-RAY DIFFRACTIONr_chiral_restr0.130.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212134
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 84 -
Rwork0.234 1527 -
obs--96.93 %

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