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- PDB-9dbb: Fe-Bound Structure of Computationally Designed Homotrimer Tet4 -

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Basic information

Entry
Database: PDB / ID: 9dbb
TitleFe-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: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Computationally Designed Tet4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6583
Polymers12,5621
Non-polymers962
Water46826
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)37,9739
Polymers37,6853
Non-polymers2886
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 area4300 Å2
ΔGint-81 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.740, 70.740, 54.080
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-

FE

21A-317-

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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.07 Å3/Da / Density % sol: 40.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 23% PEG 400, 200 mM CaCl2, 100 mM Tris (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.72195 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2024
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.72195 Å / Relative weight: 1
ReflectionResolution: 2.5→40.54 Å / Num. obs: 6985 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 71.09 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07439 / Rpim(I) all: 0.02437 / Rrim(I) all: 0.07835 / Net I/σ(I): 17.24
Reflection shellResolution: 2.5→2.591 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.9386 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1109 / CC1/2: 0.847 / CC star: 0.958 / Rpim(I) all: 0.3224 / Rrim(I) all: 0.9942 / % possible all: 99.46

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→40.54 Å / SU ML: 0.4781 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 37.3187
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2834 703 10.09 %
Rwork0.2163 6263 -
obs0.2229 6966 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.86 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 2 26 846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028847
X-RAY DIFFRACTIONf_angle_d0.48951148
X-RAY DIFFRACTIONf_chiral_restr0.0345134
X-RAY DIFFRACTIONf_plane_restr0.0037143
X-RAY DIFFRACTIONf_dihedral_angle_d20.3644315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.39521430.35971255X-RAY DIFFRACTION98.73
2.7-2.970.42151460.29511262X-RAY DIFFRACTION99.72
2.97-3.390.35831300.27951248X-RAY DIFFRACTION99.86
3.4-4.270.27131440.20551229X-RAY DIFFRACTION99.93
4.29-40.540.23671400.17781269X-RAY DIFFRACTION99.65
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)
16.75189497043-0.8181390960984.785751244149.32260795641-5.900247393196.42412731154-0.2931330429480.9282088321960.5854619617680.1130328161130.4619570378280.348604978258-0.8983584376610.21240211169-0.05816646031430.627916206586-0.101204831089-0.08435682243920.6508653312150.04035962609430.609096963974-6.44371724266-7.45581830689-4.8539727919
28.288305347344.34412656988-0.309503796564.27878151999-2.896354646528.241930565640.0542498843868-0.254394986386-0.1102226074190.9298042586130.2084028813450.679902849138-0.382007311132-0.383811330409-0.1422384554550.9370004072330.129245702718-0.04421452945820.441409802506-0.03042237304250.761689987491-7.96523446617-13.31284108957.87045546024
39.814413773942.756554651240.9264098028556.672523270493.080848470017.72533360896-0.05351656767691.12690540968-0.4677699027790.9560037100310.43368043244-0.6555837646411.353506415510.0435295371864-0.2367114785390.7616449825580.02394992268920.0009714758925060.449323950422-0.00390736430190.807053744655-6.68853060069-17.2632017394-4.66651909081
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 107 )

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