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- PDB-36cd: Crystal structure of CAT2 -

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Basic information

Entry
Database: PDB / ID: 36cd
TitleCrystal structure of CAT2
ComponentsCAT2
KeywordsTRANSCRIPTION / Transcription repressor / Biosensor / Monoterpene Indole Alkaloid (MIA) binding protein / RamR
Function / homology:
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHong, Y. / Zhang, Y.J.
Funding support United States, Denmark, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148356 United States
Novo Nordisk FoundationNNF22SA0078231 Denmark
Novo Nordisk FoundationNNF20CC0035580 Denmark
CitationJournal: Biorxiv / Year: 2026
Title: Engineering Biosensors to Enhance Monoterpene Indole Alkaloid Production in Yeast.
Authors: Holtz, M. / d'Oelsnitz, S. / Domingo, C.C. / Madsen, N.G. / Hong, M.Y. / Arnesen, J.A. / van Aalst, A.C.A. / de Haan, S. / Weingarten, C.K. / Welner, D.H. / Silver, P.A. / Zhang, Y.J. / ...Authors: Holtz, M. / d'Oelsnitz, S. / Domingo, C.C. / Madsen, N.G. / Hong, M.Y. / Arnesen, J.A. / van Aalst, A.C.A. / de Haan, S. / Weingarten, C.K. / Welner, D.H. / Silver, P.A. / Zhang, Y.J. / Jensen, M.K. / Acevedo-Rocha, C.G.
History
DepositionMay 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAT2
C: CAT2


Theoretical massNumber of molelcules
Total (without water)43,6782
Polymers43,6782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-19 kcal/mol
Surface area16750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.783, 53.924, 173.582
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 12 through 50 or (resid 51...
d_2ens_1(chain "C" and ((resid 12 through 13 and (name N...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAARGARGAA12 - 19012 - 190
d_21ALAALAALAALACB12 - 3712 - 37
d_22GLUGLUASPASPCB41 - 12441 - 124
d_23PHEPHEARGARGCB127 - 190127 - 190

NCS oper: (Code: givenMatrix: (-0.99540757478485, 0.083073484544751, 0.04756633501257), (0.067308461334596, 0.25405476899096, 0.96484493333681), (0.068068576404273, 0.96361557195727, -0. ...NCS oper: (Code: given
Matrix: (-0.99540757478485, 0.083073484544751, 0.04756633501257), (0.067308461334596, 0.25405476899096, 0.96484493333681), (0.068068576404273, 0.96361557195727, -0.25847958988622)
Vector: -6.9307015636602, 30.092654808188, -36.319517948393)

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Components

#1: Protein CAT2


Mass: 21838.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6H745
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: 2.18 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 3mg/mL of protein in a mixture of 166mM NaCl, 16mM Tris pH 8, 66mM sodium cacodylate salt pH 8, 2mM DTT, 2% PEG1000, 33mM sodium phosphate-citrate pH 5.2, and 7% ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 16, 2025
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→45.8 Å / Num. obs: 15176 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.069 / Net I/σ(I): 13.9
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1570 / CC1/2: 0.677 / Rpim(I) all: 0.548 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX2.1_6048refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→43.4 Å / SU ML: 0.3207 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2855 1513 10 %
Rwork0.2336 13610 -
obs0.2387 15123 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.41 Å2
Refinement stepCycle: LAST / Resolution: 2.43→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 0 2745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772793
X-RAY DIFFRACTIONf_angle_d0.98353778
X-RAY DIFFRACTIONf_chiral_restr0.0531427
X-RAY DIFFRACTIONf_plane_restr0.0107490
X-RAY DIFFRACTIONf_dihedral_angle_d19.0853992
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.1430778837569 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.510.33891350.271219X-RAY DIFFRACTION99.93
2.51-2.60.29531340.27721200X-RAY DIFFRACTION100
2.6-2.70.34061370.26821234X-RAY DIFFRACTION100
2.7-2.830.30021320.26191191X-RAY DIFFRACTION99.92
2.83-2.970.29711360.23741228X-RAY DIFFRACTION100
2.97-3.160.32851360.23891222X-RAY DIFFRACTION100
3.16-3.40.30831380.2531236X-RAY DIFFRACTION100
3.4-3.750.2691350.21481220X-RAY DIFFRACTION99.63
3.75-4.290.28211380.20081238X-RAY DIFFRACTION99.71
4.29-5.40.25721410.22011269X-RAY DIFFRACTION99.65
5.4-43.40.26591510.23941353X-RAY DIFFRACTION99.93

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