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- PDB-9db9: Ni-Bound Structure of Computationally Designed Homotrimer Tet4 -

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Basic information

Entry
Database: PDB / ID: 9db9
TitleNi-Bound Structure of Computationally Designed Homotrimer Tet4
ComponentsComputationally Designed Tet4
KeywordsDE NOVO PROTEIN / Metalloprotein / computational design
Function / homologyNICKEL (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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)12,6202
Polymers12,5621
Non-polymers591
Water1267
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)37,8616
Polymers37,6853
Non-polymers1763
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 area3940 Å2
ΔGint-58 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.930, 71.930, 55.780
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-

NI

21A-302-

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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.21 Å3/Da / Density % sol: 44.36 %
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: 1.48515 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: 1.48515 Å / Relative weight: 1
ReflectionResolution: 2.41→41.55 Å / Num. obs: 8250 / % possible obs: 99.98 % / Redundancy: 9.9 % / Biso Wilson estimate: 74.77 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06804 / Rpim(I) all: 0.02266 / Rrim(I) all: 0.07177 / Net I/σ(I): 18.19
Reflection shellResolution: 2.41→2.5 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.9265 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1292 / CC1/2: 0.758 / CC star: 0.929 / Rpim(I) all: 0.3083 / Rrim(I) all: 0.9773 / % 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: 2.41→41.55 Å / SU ML: 0.4033 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 34.508
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 819 9.93 %
Rwork0.2247 7428 -
obs0.2294 8247 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.18 Å2
Refinement stepCycle: LAST / Resolution: 2.41→41.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 1 7 826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0018847
X-RAY DIFFRACTIONf_angle_d0.47811148
X-RAY DIFFRACTIONf_chiral_restr0.0308134
X-RAY DIFFRACTIONf_plane_restr0.0027143
X-RAY DIFFRACTIONf_dihedral_angle_d18.8189315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.560.3711340.35571220X-RAY DIFFRACTION100
2.57-2.760.40571340.34391258X-RAY DIFFRACTION100
2.77-3.040.42241360.33571232X-RAY DIFFRACTION100
3.04-3.480.33741340.29981244X-RAY DIFFRACTION100
3.48-4.370.30841400.21341210X-RAY DIFFRACTION100
4.39-41.550.18081410.171264X-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)
16.38783099324.75025819333.585569244278.3034530538-1.177884237145.07180507715-0.5657505294321.427466879610.333041633549-0.0143429278560.8028677354040.859560335652-0.712936242376-0.470387528427-0.1468131534940.594156981322-0.087258428482-0.1079449155230.8424582807220.09760916971970.653402103021-7.02133883018-7.79045729909-6.55097167874
28.970920973811.892505385631.408837699277.8814821092-0.5241378458955.99623577366-0.191273092504-0.586729612305-0.5904765434211.290371134040.3213755418671.57445213132-0.0293819065842-0.65471756703-0.08465437292340.9660172575720.1521953842360.1253963305190.470039732369-0.05523624864141.04401214538-7.44280809677-13.65918692515.43548180791
35.621611493684.999257432734.303969818847.353585512820.9757052816026.174251450920.4173918561341.7457398215-0.4469675358490.570924367480.8706887422350.005990296691841.93991407836-0.730182078331-0.9324829687820.864904381055-0.0783124247071-0.05073184670240.887672160555-0.09082716032810.822510785159-6.55830243391-17.495487064-7.05666779197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 107 )

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