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- PDB-11mq: Crystal Structure of Fluorophore-binding Protein NovoTag657-holo -

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Basic information

Entry
Database: PDB / ID: 11mq
TitleCrystal Structure of Fluorophore-binding Protein NovoTag657-holo
ComponentsNovoTag657-holo
KeywordsDE NOVO PROTEIN / de novo designed protein / Small molecule binder / Fluorophore-binding / Multiplex Imaging
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBera, A.K. / Tran, L. / An, L. / Kang, A. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Science / Year: 2026
Title: De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging.
Authors: Tran, L. / Klein, S. / Juergens, D. / Sharma, S. / Decarreau, J. / Lee, G.R. / Wang, Y. / Chen, W. / Bera, A.K. / Kang, A. / Woods, J. / Joyce, E. / Vafeados, D.K. / Roullier, N. / Li, X. / ...Authors: Tran, L. / Klein, S. / Juergens, D. / Sharma, S. / Decarreau, J. / Lee, G.R. / Wang, Y. / Chen, W. / Bera, A.K. / Kang, A. / Woods, J. / Joyce, E. / Vafeados, D.K. / Roullier, N. / Li, X. / Liu, B. / Bo, Y. / Muratspahic, E. / Brown, T.A. / Grimm, J.B. / Patel, R. / Lavis, L.D. / Mahamid, J. / An, L. / Baker, D.
History
DepositionMar 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NovoTag657-holo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8209
Polymers15,6201
Non-polymers1,2008
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.294, 56.626, 67.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein NovoTag657-holo


Mass: 15619.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1DMM / (9P,11R)-9-(2-carboxy-3,4,5,6-tetrafluorophenyl)-14-ethyl-11,13,13,16,16-pentamethyl-2,3,5,6,7,11,12,13,14,16-decahydro-1H-pyrido[3,2,1-ij]pyrido[3',2':6,7]naphtho[2,3-f]quinolin-4-ium


Mass: 619.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H39F4N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.03 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Lithium sulfate, 0.5M Zinc acetate dihydrate, 0.1M BisTris pH 7.5, 22.5% (v/v) PEG Smear Broad. PEG Smear Broad contains: PEG1000, PEG10000, PEG2000, PEG3350, PEG400, PEG4000, PEG600, ...Details: 0.2M Lithium sulfate, 0.5M Zinc acetate dihydrate, 0.1M BisTris pH 7.5, 22.5% (v/v) PEG Smear Broad. PEG Smear Broad contains: PEG1000, PEG10000, PEG2000, PEG3350, PEG400, PEG4000, PEG600, PEG6000, PEG8000, PEG methyl ether 500, PEG methyl ether 5000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97905 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 25, 2026
RadiationMonochromator: Horizontal double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2.37→67.49 Å / Num. obs: 5424 / % possible obs: 100 % / Redundancy: 11.9 % / Biso Wilson estimate: 30.91 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.588 / Rpim(I) all: 0.187 / Net I/σ(I): 6
Reflection shellResolution: 2.37→2.46 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.361 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 561 / CC1/2: 0.36 / Rpim(I) all: 0.44 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.38 Å / SU ML: 0.3006 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.7827
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 517 9.72 %
Rwork0.2333 4803 -
obs0.2384 5320 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.06 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1100 0 68 16 1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021192
X-RAY DIFFRACTIONf_angle_d0.56491628
X-RAY DIFFRACTIONf_chiral_restr0.035171
X-RAY DIFFRACTIONf_plane_restr0.0052211
X-RAY DIFFRACTIONf_dihedral_angle_d19.7174476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.620.32531320.27011167X-RAY DIFFRACTION99.92
2.62-30.36041260.26231171X-RAY DIFFRACTION99.92
3-3.780.26361300.22351190X-RAY DIFFRACTION99.92
3.78-43.380.26031290.21731275X-RAY DIFFRACTION99.93

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