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- PDB-8vej: De novo designed cholic acid binder: CHD_buttress -

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Basic information

Entry
Database: PDB / ID: 8vej
TitleDe novo designed cholic acid binder: CHD_buttress
ComponentsCHD_buttress
KeywordsDE NOVO PROTEIN / de novo designed protein / Cholic acid / small molecule binder
Function / homologyCHOLIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.59 Å
AuthorsBera, A.K. / Tran, L. / Kang, A. / Baker, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) 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

Downloads & links

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Assembly

Deposited unit
A: CHD_buttress
B: CHD_buttress
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7664
Polymers54,9492
Non-polymers8172
Water00
1
A: CHD_buttress
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8832
Polymers27,4741
Non-polymers4091
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CHD_buttress
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8832
Polymers27,4741
Non-polymers4091
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.607, 45.962, 73.664
Angle α, β, γ (deg.)90.000, 104.050, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein CHD_buttress


Mass: 27474.471 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: Chemical ChemComp-CHD / CHOLIC ACID


Mass: 408.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H40O5 / Feature type: SUBJECT OF INVESTIGATION
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: 1.57 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium chloride 20% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 3.59→32.15 Å / Num. obs: 4921 / % possible obs: 85.78 % / Redundancy: 2.1 % / Biso Wilson estimate: 100.16 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.112 / Net I/σ(I): 4.55
Reflection shellResolution: 3.59→3.719 Å / Redundancy: 2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.51 / Num. unique obs: 483 / CC1/2: 0.822 / Rpim(I) all: 0.551 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.59→32.15 Å / SU ML: 0.4928 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1965
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 485 9.86 %
Rwork0.2396 4435 -
obs0.2434 4920 85.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.42 Å2
Refinement stepCycle: LAST / Resolution: 3.59→32.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3655 0 58 0 3713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253764
X-RAY DIFFRACTIONf_angle_d0.53645109
X-RAY DIFFRACTIONf_chiral_restr0.0314621
X-RAY DIFFRACTIONf_plane_restr0.0034642
X-RAY DIFFRACTIONf_dihedral_angle_d6.8947663
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.59-3.720.30111580.27141488X-RAY DIFFRACTION87.41
4.1-5.160.28071630.25061478X-RAY DIFFRACTION87.1
5.17-32.150.26671640.21861469X-RAY DIFFRACTION83.66
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.725551220910.122397635462-0.1739681553113.775529087710.4776431606615.19321490058-0.1650766958290.129336631021-0.353475931577-0.282728216215-0.02309136920690.4572829669280.15834602093-0.3813477149390.1778949303310.541578911962-0.0576475448716-0.04001249934770.5522353626890.006691775736750.51651825039620.357-22.736-0.907
25.316148415910.928732507570.059665834333.703942805490.8954744564782.82849175079-0.0315461082927-0.03313464438840.01254571520670.239774548678-0.09745937772270.400485090895-0.0798640906188-0.5114674007460.02689633985290.650993169617-0.05420275710810.06883166952310.5536633987090.04874322383380.5442417025811.882-3.61830.416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:252 )A3 - 252
2X-RAY DIFFRACTION2( CHAIN B AND RESID 3:252 )B3 - 252

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