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- PDB-7rkc: Computationally designed tunable C2 symmetric tandem repeat homod... -

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Basic information

Entry
Database: PDB / ID: 7rkc
TitleComputationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633
ComponentsD_3_633
KeywordsDE NOVO PROTEIN / de novo / torroid / derroid / tandem repeat / homodimer / computationally designed / C2 symmetric
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsKennedy, M.A. / Stoddard, B.L. / Hicks, D.R. / Bera, A.K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE-1762114 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139752 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG063845 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)U19AG065156 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo design of protein homodimers containing tunable symmetric protein pockets.
Authors: Hicks, D.R. / Kennedy, M.A. / Thompson, K.A. / DeWitt, M. / Coventry, B. / Kang, A. / Bera, A.K. / Brunette, T.J. / Sankaran, B. / Stoddard, B. / Baker, D.
History
DepositionJul 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D_3_633
B: D_3_633
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5517
Polymers54,2562
Non-polymers2955
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-38 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.445, 54.682, 86.987
Angle α, β, γ (deg.)90.000, 95.470, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 and (name N or name...
21(chain B and (resid 4 or (resid 5 through 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASP(chain A and ((resid 4 and (name N or name...AA49
12ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
13ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
14ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
15ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
16ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
17ASPASPARGARG(chain A and ((resid 4 and (name N or name...AA4 - 2289 - 233
21ASPASPASPASP(chain B and (resid 4 or (resid 5 through 6...BB49
22GLUGLULEULEU(chain B and (resid 4 or (resid 5 through 6...BB5 - 610 - 11
23GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
24GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
25GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231
26GLUGLUARGARG(chain B and (resid 4 or (resid 5 through 6...BB2 - 2267 - 231

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Components

#1: Protein D_3_633


Mass: 27127.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Zinc acetate, 0.1 M Na acetate pH 4.5, 10% PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 21194 / % possible obs: 96.7 % / Redundancy: 4 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Rrim(I) all: 0.092 / Χ2: 1.06 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.394.11.02911100.6580.5811.1840.607100
2.39-2.434.20.80710530.7160.4530.9280.621100
2.43-2.484.20.66510930.8050.3720.7640.641100
2.48-2.534.20.5810840.8120.3270.6680.663100
2.53-2.594.20.50310970.8710.2820.5780.702100
2.59-2.654.20.44710870.8830.2520.5140.742100
2.65-2.714.10.410760.9050.2250.4611.10199.8
2.71-2.794.20.30310950.9360.1710.3490.778100
2.79-2.874.20.23110950.960.1290.2650.874100
2.87-2.964.20.19310750.9640.1080.2211.027100
2.96-3.074.10.16511110.9730.0940.191.206100
3.07-3.194.10.14310740.9790.0810.1651.351100
3.19-3.334.10.13411050.9810.0750.1541.32599.9
3.33-3.5130.1569740.9590.10.1862.21589.9
3.51-3.732.90.219990.8830.1480.2592.67790.4
3.73-4.022.30.1296020.9620.0940.1611.95355.1
4.02-4.4240.07210860.9910.0420.0841.054100
4.42-5.064.10.05411260.9960.0310.0621.235100
5.06-6.374.10.04611190.9970.0250.0521.161100
6.37-5040.03511330.9970.020.041.19298

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.32 Å48.05 Å
Translation2.32 Å48.05 Å

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: computationally generated

Resolution: 2.35→48.05 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3119 1996 9.44 %
Rwork0.2693 19138 -
obs0.2734 21134 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 179.62 Å2 / Biso mean: 73.1269 Å2 / Biso min: 32.19 Å2
Refinement stepCycle: final / Resolution: 2.35→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 20 5 2968
Biso mean--76.22 67.25 -
Num. residues----436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1262X-RAY DIFFRACTION4.51TORSIONAL
12B1262X-RAY DIFFRACTION4.51TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.32-2.380.35741220.32371171129382
2.38-2.450.3511480.301714191567100
2.45-2.520.36171480.30314151563100
2.52-2.60.33931500.293614501600100
2.6-2.690.33861470.295514021549100
2.69-2.80.32931480.286714131561100
2.8-2.930.32291500.277514351585100
2.93-3.080.39511490.296214321581100
3.08-3.280.36311480.297214241572100
3.28-3.530.35261380.31511321145992
3.53-3.880.36171150.32551101121676
3.88-4.440.26581270.24821224135186
4.45-5.60.28751520.234314521604100
5.6-48.050.27061540.23691479163398
Refinement TLS params.Method: refined / Origin x: 10.0951 Å / Origin y: -1.0503 Å / Origin z: 23.0787 Å
111213212223313233
T0.3669 Å20.0865 Å2-0.0507 Å2-0.3383 Å2-0.0013 Å2--0.3862 Å2
L2.8229 °20.6539 °2-1.2057 °2-1.2261 °2-0.3332 °2--3.3097 °2
S-0.136 Å °0.0598 Å °0.023 Å °-0.1154 Å °0.019 Å °-0.0057 Å °-0.0578 Å °0.0656 Å °0.1088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 228
2X-RAY DIFFRACTION1allB2 - 226
3X-RAY DIFFRACTION1allD1 - 5
4X-RAY DIFFRACTION1allS1 - 7

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