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- PDB-7jh5: Co-LOCKR: de novo designed protein switch -

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Basic information

Entry
Database: PDB / ID: 7jh5
TitleCo-LOCKR: de novo designed protein switch
ComponentsCo-LOCKR: de novo designed protein switch
KeywordsDE NOVO PROTEIN / Helical bundle / protein switch
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.103 Å
AuthorsBick, M.J. / Lajoie, M.J. / Boyken, S.E. / Sankaran, B. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1629214 United States
Defense Threat Reduction Agency (DTRA)HDTRA1-18-1-0001 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2020
Title: Designed protein logic to target cells with precise combinations of surface antigens.
Authors: Lajoie, M.J. / Boyken, S.E. / Salter, A.I. / Bruffey, J. / Rajan, A. / Langan, R.A. / Olshefsky, A. / Muhunthan, V. / Bick, M.J. / Gewe, M. / Quijano-Rubio, A. / Johnson, J. / Lenz, G. / ...Authors: Lajoie, M.J. / Boyken, S.E. / Salter, A.I. / Bruffey, J. / Rajan, A. / Langan, R.A. / Olshefsky, A. / Muhunthan, V. / Bick, M.J. / Gewe, M. / Quijano-Rubio, A. / Johnson, J. / Lenz, G. / Nguyen, A. / Pun, S. / Correnti, C.E. / Riddell, S.R. / Baker, D.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Co-LOCKR: de novo designed protein switch
B: Co-LOCKR: de novo designed protein switch


Theoretical massNumber of molelcules
Total (without water)65,7602
Polymers65,7602
Non-polymers00
Water3,423190
1
A: Co-LOCKR: de novo designed protein switch


Theoretical massNumber of molelcules
Total (without water)32,8801
Polymers32,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Co-LOCKR: de novo designed protein switch


Theoretical massNumber of molelcules
Total (without water)32,8801
Polymers32,8801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.841, 52.914, 75.591
Angle α, β, γ (deg.)90.000, 102.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Co-LOCKR: de novo designed protein switch


Mass: 32879.828 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: JCSG core I B7 (0.2M di-Sodium tartrate, 20% (w/v) PEG 3350)

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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: Mar 14, 2018
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: 2.12→50 Å / Num. obs: 27665 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.094 / Rrim(I) all: 0.2 / Net I/σ(I): 7.32 / Scaling rejects: 683
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1382 / CC1/2: 0.704 / CC star: 0.909 / Rpim(I) all: 0.645 / Rrim(I) all: 1.347 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.1 Å42.99 Å
Translation2.1 Å42.99 Å

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Processing

Software
NameVersionClassification
HKL-2000714ndata scaling
PHASER2.8.1phasing
PHENIXdev 3026refinement
PDB_EXTRACT3.25data extraction
HKL-2000714ndata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational design model

Resolution: 2.103→42.381 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.288 1736 7.28 %
Rwork0.2574 22094 -
obs0.2597 23830 85.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.07 Å2 / Biso mean: 36.2963 Å2 / Biso min: 10.35 Å2
Refinement stepCycle: final / Resolution: 2.103→42.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4217 0 0 190 4407
Biso mean---32.58 -
Num. residues----564
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.103-2.16440.2871100.3121140066
2.1644-2.23430.35651130.3239139165
2.2343-2.31410.44371130.3713140666
2.3141-2.40680.31981430.2585189587
2.4068-2.51630.28651450.2513187988
2.5163-2.64890.29781480.2572187987
2.6489-2.81490.30011520.2712193990
2.8149-3.03220.29551610.2704199893
3.0322-3.33720.26841630.2352210397
3.3372-3.81980.25731590.2226201693
3.8198-4.81150.24851650.2153207094
4.8115-42.3810.28741640.2857211895

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