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- PDB-6w2r: Junction 19, DHR54-DHR79 -

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Basic information

Entry
Database: PDB / ID: 6w2r
TitleJunction 19, DHR54-DHR79
ComponentsJunction 19 DHR54-DHR79
KeywordsBIOSYNTHETIC PROTEIN / helical bundle / designed helical repeat / computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.344 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 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Junction 19 DHR54-DHR79
B: Junction 19 DHR54-DHR79
C: Junction 19 DHR54-DHR79
D: Junction 19 DHR54-DHR79


Theoretical massNumber of molelcules
Total (without water)104,9074
Polymers104,9074
Non-polymers00
Water25214
1
A: Junction 19 DHR54-DHR79


Theoretical massNumber of molelcules
Total (without water)26,2271
Polymers26,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Junction 19 DHR54-DHR79


Theoretical massNumber of molelcules
Total (without water)26,2271
Polymers26,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Junction 19 DHR54-DHR79


Theoretical massNumber of molelcules
Total (without water)26,2271
Polymers26,2271
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Junction 19 DHR54-DHR79


Theoretical massNumber of molelcules
Total (without water)26,2271
Polymers26,2271
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.674, 109.666, 81.011
Angle α, β, γ (deg.)90.000, 107.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Junction 19 DHR54-DHR79


Mass: 26226.684 Da / Num. of mol.: 4
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.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.17 Å3/Da / Density % sol: 43.25 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: Crystals were grown in Qiagen JCSG+ condition E5 (0.1M CAPS pH 10.5, 40% MPD) and required no additional cryopreservation

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid nitrogen vapor stream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2017
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.344→50 Å / Num. obs: 36576 / % possible obs: 97.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 48.92 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.033 / Rrim(I) all: 0.078 / Χ2: 0.954 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.393.91.04615730.5090.5641.1960.83484.4
2.39-2.434.31.07217170.620.5591.2150.85591.5
2.43-2.484.91.10517650.7270.5451.2360.8795.8
2.48-2.535.30.94718020.8280.4461.0480.84796.2
2.53-2.595.50.87918030.8440.4040.9680.8596.4
2.59-2.655.60.73818210.8960.3360.8120.87197.3
2.65-2.715.60.62818210.9030.2860.6910.90197.5
2.71-2.795.60.53518430.9390.2440.5890.89698.3
2.79-2.875.70.41918370.9650.1910.4610.95398.1
2.87-2.965.70.3118470.9730.1420.3420.93298.6
2.96-3.075.70.22718540.9870.1030.250.9699.1
3.07-3.195.80.16918640.9910.0770.1851.02499.2
3.19-3.335.90.15418600.990.0690.1691.02999.4
3.33-3.515.90.11118540.9930.050.1221.00499.3
3.51-3.735.90.08218570.9960.0370.09199.4
3.73-4.025.80.06118710.9980.0280.0670.96399.7
4.02-4.425.70.04818940.9980.0220.0531.08699.5
4.42-5.065.80.04218720.9990.0190.0461.0599.7
5.06-6.3760.04518900.9990.020.051.02399.7
6.37-505.90.0319310.9990.0140.0330.97899.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.34 Å46.39 Å
Translation2.34 Å46.39 Å

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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: 2.344→46.386 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 35.19
RfactorNum. reflection% reflection
Rfree0.2741 1795 5.5 %
Rwork0.2435 --
obs0.2452 32657 86.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 385.92 Å2 / Biso mean: 80.0808 Å2 / Biso min: 28.72 Å2
Refinement stepCycle: final / Resolution: 2.344→46.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5701 0 0 14 5715
Biso mean---55.57 -
Num. residues----863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035711
X-RAY DIFFRACTIONf_angle_d0.3957786
X-RAY DIFFRACTIONf_chiral_restr0.0311039
X-RAY DIFFRACTIONf_plane_restr0.0021022
X-RAY DIFFRACTIONf_dihedral_angle_d13.263593
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.344-2.40690.4035990.3938164361
2.4069-2.47780.38141090.3351191670
2.4778-2.55770.33271120.3263204375
2.5577-2.64910.33261270.307210678
2.6491-2.75520.35461380.2886225883
2.7552-2.88060.34391330.279232086
2.8806-3.03240.28091490.2557249691
3.0324-3.22230.28321500.254256394
3.2223-3.47110.30531520.265262196
3.4711-3.82020.25451600.2278271998
3.8202-4.37270.23471520.1917269499
4.3727-5.50770.20611550.2289272699
5.5077-46.3860.2871590.234275799
Refinement TLS params.Method: refined / Origin x: -3.4215 Å / Origin y: 31.3397 Å / Origin z: 12.0702 Å
111213212223313233
T0.4336 Å2-0.0181 Å20.0525 Å2-0.4015 Å2-0.0013 Å2--0.3476 Å2
L0.1593 °20.1784 °20.5206 °2-0.0645 °2-0.0408 °2--1.318 °2
S-0.0512 Å °-0.019 Å °0.0179 Å °-0.0419 Å °0.0709 Å °-0.0347 Å °-0.4024 Å °-0.0832 Å °-0.0139 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 219
2X-RAY DIFFRACTION1allB2 - 222
3X-RAY DIFFRACTION1allC3 - 216
4X-RAY DIFFRACTION1allD2 - 213
5X-RAY DIFFRACTION1allS1 - 14

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