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- PDB-9dbc: Mn-Bound Structure of Computationally Designed Homotrimer Tet4 -

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Basic information

Entry
Database: PDB / ID: 9dbc
TitleMn-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: 2.3 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)12,6172
Polymers12,5621
Non-polymers551
Water41423
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)37,8506
Polymers37,6853
Non-polymers1653
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 area3960 Å2
ΔGint-49 kcal/mol
Surface area15440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.920, 71.920, 55.490
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-

MN

21A-314-

HOH

31A-322-

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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG 400, 200 mM (NH4)2SO4, 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: 1.12703 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12703 Å / Relative weight: 1
ReflectionResolution: 2.3→41.43 Å / Num. obs: 9531 / % possible obs: 99.87 % / Redundancy: 10.2 % / Biso Wilson estimate: 71.71 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.05065 / Rpim(I) all: 0.01657 / Rrim(I) all: 0.05332 / Net I/σ(I): 22.27
Reflection shellResolution: 2.3→2.383 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.152 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 1493 / CC1/2: 0.76 / CC star: 0.929 / Rpim(I) all: 0.4012 / Rrim(I) all: 1.222 / % possible all: 99.16

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→41.43 Å / SU ML: 0.4661 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 36.8804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2618 953 10.04 %
Rwork0.2063 8541 -
obs0.212 9494 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.44 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms832 0 1 23 856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034856
X-RAY DIFFRACTIONf_angle_d0.48091159
X-RAY DIFFRACTIONf_chiral_restr0.0318135
X-RAY DIFFRACTIONf_plane_restr0.0032145
X-RAY DIFFRACTIONf_dihedral_angle_d15.8828314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.420.42541370.38411229X-RAY DIFFRACTION98.84
2.42-2.570.35781320.33881206X-RAY DIFFRACTION100
2.57-2.770.39041360.32441220X-RAY DIFFRACTION100
2.77-3.050.39661420.28541227X-RAY DIFFRACTION99.78
3.05-3.490.36281340.26971246X-RAY DIFFRACTION100
3.49-4.40.2481300.17721199X-RAY DIFFRACTION99.92
4.4-41.430.18481420.15531214X-RAY DIFFRACTION99.85
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)
16.807977457430.2814062830965.892008476796.07782569874-3.020479712126.86641290162-0.7734821244931.784620053180.203336485151-0.7620802118070.9980523570760.461138785483-0.8885416778280.539287579503-0.2521197467610.68594578153-0.262798896225-0.03267401204130.858811034767-0.04203395737760.682888319804-5.16650890056-7.7345612639523.4246941811
27.242859344043.044680926130.917389656057.882646551830.7776698158367.14116607744-1.60929912283-0.798789546702-0.7083629019191.68408688411.084282422780.6162306877091.11145114122-0.596823858050.4154029897720.9301754915370.2229493103420.04678231972020.6522967909920.02275584275120.693572539819-9.01711573124-12.538377273437.6856168581
34.244707493833.690370537194.601211904729.262980877522.754877729436.88120135505-0.6693251138742.04303697905-0.9814231273060.2277852852480.929912386548-0.03415146331031.72181143609-1.236049319770.5616935870120.89055472419-0.2847590939440.1097967030290.695896824418-0.1736686571750.692627305348-8.29031694351-16.811295622725.3386934737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 80 )
3X-RAY DIFFRACTION3chain 'A' and (resid 81 through 109 )

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