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- PDB-7mwq: Structure of De Novo designed beta sheet heterodimer LHD29A53/B53 -

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Basic information

Entry
Database: PDB / ID: 7mwq
TitleStructure of De Novo designed beta sheet heterodimer LHD29A53/B53
Components
  • LHD29A53
  • LHD29B53
KeywordsDE NOVO PROTEIN / de novo design / beta-sheet / heterodimer
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsBera, A.K. / Sahtoe, D.D. / Kang, A. / Praetorius, F. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2022
Title: Reconfigurable asymmetric protein assemblies through implicit negative design.
Authors: Sahtoe, D.D. / Praetorius, F. / Courbet, A. / Hsia, Y. / Wicky, B.I.M. / Edman, N.I. / Miller, L.M. / Timmermans, B.J.R. / Decarreau, J. / Morris, H.M. / Kang, A. / Bera, A.K. / Baker, D.
History
DepositionMay 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 16, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LHD29A53
B: LHD29B53
C: LHD29A53
D: LHD29B53


Theoretical massNumber of molelcules
Total (without water)92,3534
Polymers92,3534
Non-polymers00
Water25214
1
A: LHD29A53
D: LHD29B53


Theoretical massNumber of molelcules
Total (without water)46,1762
Polymers46,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-6 kcal/mol
Surface area20370 Å2
MethodPISA
2
C: LHD29A53

B: LHD29B53


Theoretical massNumber of molelcules
Total (without water)46,1762
Polymers46,1762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1870 Å2
ΔGint-8 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.315, 73.454, 74.149
Angle α, β, γ (deg.)108.396, 106.702, 110.152
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein LHD29A53


Mass: 22983.434 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: Protein LHD29B53


Mass: 23192.820 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)
#3: 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium Iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99991 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99991 Å / Relative weight: 1
ReflectionResolution: 2.56→51.56 Å / Num. obs: 32600 / % possible obs: 97.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 58.44 Å2 / CC1/2: 0.991 / Net I/σ(I): 4.7
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2389 / CC1/2: 0.651 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Adxvdata collection
DIALSdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Design model

Resolution: 2.56→51.56 Å / SU ML: 0.4518 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.5726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 1666 5.12 %
Rwork0.2334 30887 -
obs0.2353 32553 97.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.6 Å2
Refinement stepCycle: LAST / Resolution: 2.56→51.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6370 0 0 14 6384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026418
X-RAY DIFFRACTIONf_angle_d0.38538604
X-RAY DIFFRACTIONf_chiral_restr0.03271006
X-RAY DIFFRACTIONf_plane_restr0.00281124
X-RAY DIFFRACTIONf_dihedral_angle_d13.7442592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.630.40251400.37382360X-RAY DIFFRACTION90.58
2.63-2.720.40381680.35692535X-RAY DIFFRACTION97.51
2.72-2.820.39181220.31242588X-RAY DIFFRACTION98.05
2.82-2.930.34191510.29832585X-RAY DIFFRACTION98.24
2.93-3.060.35311330.28992601X-RAY DIFFRACTION98.17
3.06-3.220.32881420.27272604X-RAY DIFFRACTION98.39
3.22-3.420.31711480.25282554X-RAY DIFFRACTION98.36
3.42-3.690.26451460.22232610X-RAY DIFFRACTION98.78
3.69-4.060.23481580.20672583X-RAY DIFFRACTION98.99
4.06-4.650.23911670.19342580X-RAY DIFFRACTION99.03
4.65-5.850.2144810.22742663X-RAY DIFFRACTION99.24
5.85-51.560.21581100.19722624X-RAY DIFFRACTION97.96

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