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- PDB-8vei: De novo designed colic acid binder CHD_r1 -

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Basic information

Entry
Database: PDB / ID: 8vei
TitleDe novo designed colic acid binder CHD_r1
ComponentsCHD_r1
KeywordsDE NOVO PROTEIN / de novo designed protein / Small molecule binder / colic acid
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsBera, A.K. / An, L. / Baker, D.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Bill & Melinda Gates Foundation United States
CitationJournal: Science / Year: 2024
Title: Binding and sensing diverse small molecules using shape-complementary pseudocycles.
Authors: An, L. / Said, M. / Tran, L. / Majumder, S. / Goreshnik, I. / Lee, G.R. / Juergens, D. / Dauparas, J. / Anishchenko, I. / Coventry, B. / Bera, A.K. / Kang, A. / Levine, P.M. / Alvarez, V. / ...Authors: An, L. / Said, M. / Tran, L. / Majumder, S. / Goreshnik, I. / Lee, G.R. / Juergens, D. / Dauparas, J. / Anishchenko, I. / Coventry, B. / Bera, A.K. / Kang, A. / Levine, P.M. / Alvarez, V. / Pillai, A. / Norn, C. / Feldman, D. / Zorine, D. / Hicks, D.R. / Li, X. / Sanchez, M.G. / Vafeados, D.K. / Salveson, P.J. / Vorobieva, A.A. / Baker, D.
History
DepositionDec 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHD_r1


Theoretical massNumber of molelcules
Total (without water)14,7961
Polymers14,7961
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.242, 57.819, 85.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein CHD_r1


Mass: 14795.930 Da / Num. of mol.: 1
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.: 33 / Source method: obtained synthetically / Formula: H2O
Has ligand of interestY

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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: 1.99 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/Biocine pH 8.5, 25% v/v 2-methyl-2,4-pentanediol (MPD); 25% PEG1000; 25% w/v PEG 3350 and 0.093 MSodium fluoride; 0.3 M Sodium bromide; 0.3 M Sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.03→46.24 Å / Num. obs: 7672 / % possible obs: 99.79 % / Redundancy: 12.8 % / Biso Wilson estimate: 40.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.247 / Rpim(I) all: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 2.03→2.18 Å / Redundancy: 12.8 % / Rmerge(I) obs: 1.42 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1480 / CC1/2: 0.831 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.56 Å / SU ML: 0.2742 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 33.8099
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 766 10 %
Rwork0.227 6896 -
obs0.231 7662 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.43 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 0 33 1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221020
X-RAY DIFFRACTIONf_angle_d0.43181369
X-RAY DIFFRACTIONf_chiral_restr0.0318144
X-RAY DIFFRACTIONf_plane_restr0.0015167
X-RAY DIFFRACTIONf_dihedral_angle_d3.9126129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.180.34141490.30611338X-RAY DIFFRACTION97.96
2.18-2.40.29791490.2571340X-RAY DIFFRACTION99.87
2.4-2.750.2621520.22761375X-RAY DIFFRACTION99.87
2.75-3.460.26261540.22971386X-RAY DIFFRACTION99.94
3.47-42.560.25261620.21261457X-RAY DIFFRACTION99.75
Refinement TLS params.Method: refined / Origin x: 11.6843561602 Å / Origin y: 10.9232403703 Å / Origin z: -12.6665886613 Å
111213212223313233
T0.330569770308 Å20.0223604750191 Å20.00733793639888 Å2-0.305658648807 Å2-0.0858620440425 Å2--0.473953718281 Å2
L4.26784342029 °20.724353040719 °20.603591942695 °2-3.33447505661 °20.200065089376 °2--2.69278259315 °2
S-0.110213854237 Å °-0.430333255246 Å °0.447037837038 Å °0.189053050291 Å °0.000860228491487 Å °0.294382323318 Å °-0.072832034235 Å °-0.233584861019 Å °0.11984614254 Å °
Refinement TLS groupSelection details: ALL

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