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- PDB-9dba: Co-Bound Structure of Computationally Designed Homotrimer Tet4 -

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Basic information

Entry
Database: PDB / ID: 9dba
TitleCo-Bound Structure of Computationally Designed Homotrimer Tet4
ComponentsComputationally Designed Tet4
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHoffnagle, A.M. / Tezcan, F.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM138884 United States
CitationJournal: Biochemistry / Year: 2025
Title: A De Novo Designed Protein with Versatile Metal Binding and Tunable Hydrolytic Activity.
Authors: Hoffnagle, A.M. / Srisantitham, S. / Neeley, M. / Tsai, C.Y. / Tezcan, F.A.
History
DepositionAug 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Computationally Designed Tet4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6212
Polymers12,5621
Non-polymers591
Water61334
1
A: Computationally Designed Tet4
hetero molecules

A: Computationally Designed Tet4
hetero molecules

A: Computationally Designed Tet4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8626
Polymers37,6853
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3780 Å2
ΔGint-56 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.260, 72.260, 56.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Components on special symmetry positions
IDModelComponents
11A-201-

CO

21A-324-

HOH

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Components

#1: Protein Computationally Designed Tet4


Mass: 12561.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 400, 200 mM NaCl, 100 mM Bis-Tris (pH 5.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.60513 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.60513 Å / Relative weight: 1
ReflectionResolution: 2.2→42.07 Å / Num. obs: 10609 / % possible obs: 99.5 % / Redundancy: 4.8 % / Biso Wilson estimate: 46.36 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04053 / Rpim(I) all: 0.02036 / Rrim(I) all: 0.04547 / Net I/σ(I): 28.94
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.1621 / Mean I/σ(I) obs: 6.63 / Num. unique obs: 1594 / CC1/2: 0.967 / CC star: 0.992 / Rpim(I) all: 0.1008 / Rrim(I) all: 0.1923 / % possible all: 97.82

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.07 Å / SU ML: 0.3332 / Cross valid method: FREE R-VALUE / σ(F): 2.06 / Phase error: 33.7214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2823 1064 10.03 %
Rwork0.2266 9545 -
obs0.232 10609 94.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 1 34 853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035840
X-RAY DIFFRACTIONf_angle_d0.67551137
X-RAY DIFFRACTIONf_chiral_restr0.0321133
X-RAY DIFFRACTIONf_plane_restr0.0034141
X-RAY DIFFRACTIONf_dihedral_angle_d17.5053310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.43351250.36051081X-RAY DIFFRACTION87.01
2.3-2.420.37041300.33171181X-RAY DIFFRACTION93.91
2.42-2.570.37671340.33251219X-RAY DIFFRACTION95.01
2.57-2.770.34131330.32981210X-RAY DIFFRACTION96.2
2.77-3.050.33891390.28421208X-RAY DIFFRACTION96.08
3.05-3.490.28111410.24731210X-RAY DIFFRACTION96.64
3.49-4.390.26561300.18021189X-RAY DIFFRACTION95.3
4.4-42.070.21331320.16911247X-RAY DIFFRACTION96.43
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.669054110054.493714551484.7463903799511.4964904067-1.181655078296.35976734803-0.8316828856451.987198135571.50955347646-0.2643649850611.278040299683.05425447551-0.935153040691-0.687052920572-0.2686198487460.481641244515-0.02450069784970.05177581222360.4737688970230.2019425282440.815807635973-8.45199601329-8.16325404829-1.75964037261
26.064054774593.597424985643.2680439654611.2459820978-1.770017505147.17623599094-0.1904252131571.04615315722-0.474218722990.5303967729910.8375101249630.8069753944480.929732755902-0.298245983349-0.2443398955490.466802391578-0.0380540301723-0.01114384738620.386892186681-0.07024560561090.57941617347-5.88064294567-16.16759327280.0265840321548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 107 )

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