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- PDB-9db8: Cu-Bound Structure of Computationally Designed Homotrimer Tet4 -

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Basic information

Entry
Database: PDB / ID: 9db8
TitleCu-Bound Structure of Computationally Designed Homotrimer Tet4
ComponentsComputationally Designed Tet4
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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

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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)12,6653
Polymers12,5621
Non-polymers1042
Water28816
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)37,9969
Polymers37,6853
Non-polymers3116
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 area4110 Å2
ΔGint-73 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.360, 72.360, 56.540
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-

CU

21A-310-

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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / 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.: 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% PEG 400, 200 mM CaCl2, 100 mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12709 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: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.206→41.98 Å / Num. obs: 11107 / % possible obs: 99.84 % / Redundancy: 9.7 % / Biso Wilson estimate: 64.32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.05016 / Rpim(I) all: 0.01742 / Rrim(I) all: 0.05317 / Net I/σ(I): 22.17
Reflection shellResolution: 2.206→2.285 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.8737 / Mean I/σ(I) obs: 2.55 / Num. unique obs: 1828 / CC1/2: 0.732 / CC star: 0.919 / Rpim(I) all: 0.285 / Rrim(I) all: 0.9195 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→41.98 Å / SU ML: 0.4418 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 36.43
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 1104 9.94 %
Rwork0.2235 9999 -
obs0.2284 11103 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.44 Å2
Refinement stepCycle: LAST / Resolution: 2.21→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 2 16 836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021840
X-RAY DIFFRACTIONf_angle_d0.49391137
X-RAY DIFFRACTIONf_chiral_restr0.0327133
X-RAY DIFFRACTIONf_plane_restr0.0033141
X-RAY DIFFRACTIONf_dihedral_angle_d20.2684310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.310.42411360.37051262X-RAY DIFFRACTION99.86
2.31-2.430.36681380.31371268X-RAY DIFFRACTION100
2.43-2.580.35211340.29781230X-RAY DIFFRACTION100
2.58-2.780.34451380.28881275X-RAY DIFFRACTION99.93
2.78-3.060.36591440.29951241X-RAY DIFFRACTION99.93
3.06-3.50.33631320.26391242X-RAY DIFFRACTION100
3.5-4.40.24431340.20391225X-RAY DIFFRACTION99.34
4.41-41.980.21531480.17361256X-RAY DIFFRACTION99.01
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)
13.38155733426-0.6134404301051.459482239327.945723288742.969623486783.68570372998-0.752139718764-1.07009688071-0.5177713814470.8996303847810.6651874898520.1603942693310.4785280940691.072914509120.07611869891720.9243468399040.1574706550140.03710466184990.5354328713410.01105953612630.694767319847-4.49170839928-14.64160617164.22738402861
26.02222603783.898384066752.144255115347.133874896350.2669560400164.86595681375-0.3911029052781.54295980584-1.45307474215-0.2634737898490.482804492864-0.1642049105841.30950281781-0.391999160931-0.405179692890.824291256896-0.179775008273-0.07316925964280.874209156729-0.228870983430.705762474806-7.1412008224-17.1833961254-5.59414307799
39.682283362473.82141782491-4.208968092077.64920229086-4.676303586228.730642067670.0152899956212.165225407841.08420714656-0.5553258520230.7064355513671.27262050155-1.28427958768-1.4744799541-0.339570595290.630416400291-0.039158475812-0.1499961025510.7258706577270.1499418142860.770922740256-10.6968858451-8.42492607286-6.75499378123
47.82263643724-1.490175425825.16542861355.18845156854-2.080250801135.10122116731-0.6501321941030.2480737003070.1793801450940.5402852063590.6529597695060.382648658716-0.5263413395410.336575936227-0.3295654840620.805582430545-0.175185910186-0.09311152224690.4772398577630.09992790657960.668221505151-5.19852233171-7.05902084933-3.30843481708
52.62229599033-1.22773554567-2.062737053042.847572533821.473337440712.601358716880.6082536047930.3384389542720.7352724953510.1258129869410.973428155108-0.943910414571-1.86953958876-0.2386164940130.5354492604852.248916188851.476188296391.32618260662.32532523834-0.5224129673211.2150574658-18.1337573724-10.620940903417.0029587108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 56 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 107 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 18 )
4X-RAY DIFFRACTION4chain 'A' and (resid 19 through 49 )
5X-RAY DIFFRACTION5chain 'A' and (resid 50 through 55 )

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