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- PDB-6w2w: Junction 24, DHR14-DHR18 -

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Basic information

Entry
Database: PDB / ID: 6w2w
TitleJunction 24, DHR14-DHR18
ComponentsJunction 24 DHR14-DHR18
KeywordsBIOSYNTHETIC PROTEIN / Designed helical repeat / computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsBick, M.J. / Brunette, T.J. / Baker, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Modular repeat protein sculpting using rigid helical junctions.
Authors: Brunette, T.J. / Bick, M.J. / Hansen, J.M. / Chow, C.M. / Kollman, J.M. / Baker, D.
History
DepositionMar 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Junction 24 DHR14-DHR18


Theoretical massNumber of molelcules
Total (without water)26,7221
Polymers26,7221
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, Protein was determined to be monomeric by SAXS, with an expected radius of gyration and a Vr score that indicates the protein in solution closely matches the design.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.091, 49.675, 92.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Junction 24 DHR14-DHR18


Mass: 26721.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.42 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Crystals were grown in Qiagen JCSG+ suite condition D9 (0.19M Ammonium sulfate, 25.5% (w/v) PEG 4000, 15% (v/v) glycerol) and required no additional cryopreservation

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen cryo stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2017
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13697 / % possible obs: 99.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 43.57 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 0.738 / Net I/σ(I): 6.2 / Num. measured all: 77173
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.91.3266130.6070.7021.5070.48190.5
2.14-2.184.51.3886660.5120.6891.5570.51396.9
2.18-2.225.21.116490.6430.5221.2310.49499.2
2.22-2.265.50.8896860.6950.4120.9830.54399.4
2.26-2.315.80.7666580.7530.3470.8440.53100
2.31-2.375.90.6196910.8450.2760.6790.55100
2.37-2.4260.5046630.8980.2250.5530.53100
2.42-2.4960.4126840.9350.1850.4530.534100
2.49-2.5660.3236750.9510.1450.3550.567100
2.56-2.6560.2966810.9590.1330.3250.575100
2.65-2.7460.2436790.9660.110.2670.615100
2.74-2.855.90.1846690.9740.0830.2020.721100
2.85-2.985.90.1517070.9860.0680.1660.766100
2.98-3.145.90.1196840.990.0530.1310.931100
3.14-3.335.90.0946970.9940.0430.1040.977100
3.33-3.595.80.0766870.9930.0340.0831.019100
3.59-3.955.70.0656920.9970.030.0721.02100
3.95-4.525.60.0467180.9970.0210.0511.051100
4.52-5.75.70.0397100.9980.0180.0430.975100
5.7-505.40.0327880.9990.0150.0351.11399.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-20002.3.10data scaling
PHASER2.8.0phasing
PHENIXdev-2849refinement
PDB_EXTRACT3.25data extraction
HKL-20002.3.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.21→43.714 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.26
RfactorNum. reflection% reflection
Rfree0.2548 1110 9.87 %
Rwork0.2289 --
obs0.2315 11245 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.36 Å2 / Biso mean: 70.8442 Å2 / Biso min: 32.38 Å2
Refinement stepCycle: final / Resolution: 2.21→43.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 0 20 1537
Biso mean---50.62 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021528
X-RAY DIFFRACTIONf_angle_d0.4172087
X-RAY DIFFRACTIONf_chiral_restr0.029270
X-RAY DIFFRACTIONf_plane_restr0.002277
X-RAY DIFFRACTIONf_dihedral_angle_d16.434973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.21-2.31060.34721220.3159112687
2.3106-2.43240.3581270.2754118591
2.4324-2.58480.27421300.2741122493
2.5848-2.78430.33321400.2689124096
2.7843-3.06450.29721440.2503128997
3.0645-3.50770.26411450.2206131499
3.5077-4.41870.20111470.19531333100
4.4187-43.7140.24071550.2191424100
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)
15.13990.43564.17053.03720.2856.98810.2652-0.1515-0.42010.36620.1087-0.24240.3891-0.1468-0.38910.63550.02790.01790.49410.06790.4688-12.858-27.20810.396
29.60532.92635.0545.31582.4347.4159-0.1438-0.75460.24480.65440.01450.16850.4094-0.38250.05870.45430.0560.03880.6917-0.01330.4323-14.766-17.54210.413
34.72150.11932.53646.1773-1.31242.6502-0.11350.3294-0.1232-0.41750.0711-0.69020.83790.23020.0250.33270.03030.07260.496-0.07360.4289-8.209-16.4123.095
46.67184.0792.70614.62830.72556.7594-0.3877-0.22860.43440.13990.04950.2141-0.5894-0.22580.32610.41940.1662-0.01460.38820.01290.3304-4.416-4.43810.202
58.2461.132-0.7383.8684-1.0335.5215-0.19880.2740.7599-0.0330.01350.3931-1.1565-1.15560.09240.66760.3209-0.04740.698-0.12320.4498-10.7641.1196.024
67.40170.8358-1.37656.193-0.07994.03390.3446-0.0121-0.06240.6244-0.1113-0.7815-1.4401-0.9752-0.10221.18630.46540.02750.7368-0.08940.5987-7.9585.71314.992
71.901-0.22981.21050.26380.03291.84870.0135-0.3982-0.45060.0578-0.1484-0.1378-1.6941-1.67440.06791.55690.8215-0.11550.93370.04740.7711-15.8767.5279.668
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:43 )A4 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:63 )A44 - 63
3X-RAY DIFFRACTION3( CHAIN A AND RESID 64:83 )A64 - 83
4X-RAY DIFFRACTION4( CHAIN A AND RESID 84:139 )A84 - 139
5X-RAY DIFFRACTION5( CHAIN A AND RESID 140:169 )A140 - 169
6X-RAY DIFFRACTION6( CHAIN A AND RESID 170:199 )A170 - 199
7X-RAY DIFFRACTION7( CHAIN A AND RESID 200:227 )A200 - 227

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