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- PDB-6w2q: Junction 34, DHR53-DHR4 -

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Basic information

Entry
Database: PDB / ID: 6w2q
TitleJunction 34, DHR53-DHR4
ComponentsJunction 34
KeywordsBIOSYNTHETIC PROTEIN / helical bundle / designed helical repeat / computational design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Junction 34
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3912
Polymers24,3511
Non-polymers401
Water1,74797
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)43.934, 57.578, 71.729
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 34


Mass: 24350.592 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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.86 Å3/Da / Density % sol: 33.97 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals were grown in Qiagen JCSG Core III suite condition G5 (0.2M calcium chloride dihydrate, 20% (w/v) PEG 3500). Crystals were briefly soaked in crystallization condition supplemented ...Details: Crystals were grown in Qiagen JCSG Core III suite condition G5 (0.2M calcium chloride dihydrate, 20% (w/v) PEG 3500). Crystals were briefly soaked in crystallization condition supplemented with 25% (v/v) PEG 400 as a cryoprotectant

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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: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2016
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 18766 / % possible obs: 99.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.029 / Rrim(I) all: 0.076 / Χ2: 0.791 / Net I/σ(I): 7.9 / Num. measured all: 124942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.785.31.7419200.280.8171.930.44799.4
1.78-1.816.21.6368980.4430.711.7870.47797.8
1.81-1.856.61.269160.5640.5241.3670.48599.3
1.85-1.896.71.0879160.7080.4481.1780.52398.9
1.89-1.936.80.8319140.7510.3410.8990.5598.4
1.93-1.976.80.6629100.8210.2720.7170.5499.9
1.97-2.026.80.4689300.9010.1920.5070.56198.8
2.02-2.076.80.3569210.930.1460.3850.64899
2.07-2.146.80.2779300.970.1140.30.69799.3
2.14-2.26.80.2199390.970.090.2370.78899.8
2.2-2.286.90.1889160.9820.0770.2030.91299.5
2.28-2.386.90.1579250.9860.0640.170.98599.5
2.38-2.486.90.1449510.9890.0590.1551.01199.7
2.48-2.616.90.129370.9890.0490.131.02299.6
2.61-2.786.90.1039450.9910.0420.1111.02599.8
2.78-2.996.80.0889460.9940.0360.0951.01199.9
2.99-3.296.80.0719540.9960.0290.0770.97199.8
3.29-3.776.60.0579660.9970.0240.0621.08899.9
3.77-4.756.70.0489780.9960.020.0520.964100
4.75-506.40.0310540.9990.0130.0330.90799.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.98 Å44.9 Å
Translation3.98 Å44.9 Å

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Processing

Software
NameVersionClassification
HKL-20002.3.10data scaling
PHASER2.7.18phasing
PHENIXdev-2611refinement
PDB_EXTRACT3.25data extraction
HKL-20002.3.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 1.8→44.901 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 23.3
Details: Iterative rounds of manual model building in Coot and refinement in Phenix.
RfactorNum. reflection% reflection
Rfree0.2264 1648 10.01 %
Rwork0.2012 --
obs0.2038 16463 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.73 Å2 / Biso mean: 41.0369 Å2 / Biso min: 19.71 Å2
Refinement stepCycle: final / Resolution: 1.8→44.901 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 1 97 1511
Biso mean--53.79 43.91 -
Num. residues----196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031446
X-RAY DIFFRACTIONf_angle_d0.4911963
X-RAY DIFFRACTIONf_chiral_restr0.035249
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d14.785932
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8530.36791090.3059102879
1.853-1.91280.26241210.2886107483
1.9128-1.98110.29641210.256111688
1.9811-2.06050.29871320.2367120293
2.0605-2.15420.21341370.2033123897
2.1542-2.26780.24581440.1867126698
2.2678-2.40990.23421420.1932127197
2.4099-2.59590.22261450.2127298
2.5959-2.85710.19321440.1859128099
2.8571-3.27050.22861480.2039131899
3.2705-4.120.21291480.17251340100
4.12-44.9010.21941570.20951410100
Refinement TLS params.Method: refined / Origin x: 31.6084 Å / Origin y: 20.8636 Å / Origin z: 51.2367 Å
111213212223313233
T0.2139 Å20.0005 Å20.0266 Å2-0.2269 Å20.0117 Å2--0.2198 Å2
L0.7929 °2-0.0755 °20.0316 °2-1.8716 °20.3544 °2--0.7995 °2
S0.1566 Å °-0.0159 Å °0.0387 Å °-0.0884 Å °-0.1626 Å °-0.1147 Å °-0.0546 Å °-0.0411 Å °-0.0001 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 9 through 204)

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