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- PDB-6uup: Structure of anti-hCD33 conditional scFv -

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Basic information

Entry
Database: PDB / ID: 6uup
TitleStructure of anti-hCD33 conditional scFv
ComponentsAnti-CD33 conditional scFv
KeywordsANTITUMOR PROTEIN / Conditional CAR / MTX / CD33 / conditional antibody
Function / homology: / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesCamelidae mixed library (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2000186 Å
AuthorsKimberlin, C.R. / Park, S.
CitationJournal: Nat Commun / Year: 2021
Title: Direct control of CAR T cells through small molecule-regulated antibodies.
Authors: Park, S. / Pascua, E. / Lindquist, K.C. / Kimberlin, C. / Deng, X. / Mak, Y.S.L. / Melton, Z. / Johnson, T.O. / Lin, R. / Boldajipour, B. / Abraham, R.T. / Pons, J. / Sasu, B.J. / Van ...Authors: Park, S. / Pascua, E. / Lindquist, K.C. / Kimberlin, C. / Deng, X. / Mak, Y.S.L. / Melton, Z. / Johnson, T.O. / Lin, R. / Boldajipour, B. / Abraham, R.T. / Pons, J. / Sasu, B.J. / Van Blarcom, T.J. / Chaparro-Riggers, J.
History
DepositionOct 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Anti-CD33 conditional scFv
B: Anti-CD33 conditional scFv
C: Anti-CD33 conditional scFv
D: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,52037
Polymers113,7884
Non-polymers2,73133
Water12,737707
1
A: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,36812
Polymers28,4471
Non-polymers92111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7235
Polymers28,4471
Non-polymers2764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,27611
Polymers28,4471
Non-polymers82910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Anti-CD33 conditional scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1529
Polymers28,4471
Non-polymers7058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.234, 104.635, 87.915
Angle α, β, γ (deg.)90.000, 113.572, 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

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Antibody , 1 types, 4 molecules ABCD

#1: Antibody
Anti-CD33 conditional scFv


Mass: 28447.072 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 740 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 707 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tis pH 8.5, 2% Tacsimate pH 8, 16%w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.2→46.3 Å / Num. obs: 68385 / % possible obs: 99.92 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.0418909685 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1919 / Rpim(I) all: 0.07859 / Rrim(I) all: 0.2076 / Net I/σ(I): 9.84
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 7 % / Rmerge(I) obs: 1.305 / Num. unique obs: 6782 / CC1/2: 0.634 / Rpim(I) all: 0.5298 / Rrim(I) all: 1.41 / % possible all: 99.88

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ouo

4ouo


Resolution: 2.2000186→46.2394440038 Å / SU ML: 0.314986693358 / Cross valid method: FREE R-VALUE / σ(F): 1.33737795507 / Phase error: 25.6928542161
RfactorNum. reflection% reflection
Rfree0.236525970988 1540 2.25314196257 %
Rwork0.197033939664 --
obs0.19790491114 68349 99.9283604784 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33.5758185558 Å2
Refinement stepCycle: LAST / Resolution: 2.2000186→46.2394440038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 166 707 7645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002219304430717057
X-RAY DIFFRACTIONf_angle_d0.5010706168339538
X-RAY DIFFRACTIONf_chiral_restr0.04226110409071014
X-RAY DIFFRACTIONf_plane_restr0.003258560463641215
X-RAY DIFFRACTIONf_dihedral_angle_d4.057883548874051
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2000186-2.2710.3035169161891520.2807513328126017X-RAY DIFFRACTION99.9352016848
2.271-2.35220.2984576282231290.2736189793526054X-RAY DIFFRACTION99.935348311
2.3522-2.44640.3443314940671500.263133493836067X-RAY DIFFRACTION100
2.4464-2.55770.2676727289021350.2423296168266026X-RAY DIFFRACTION99.9837715028
2.5577-2.69250.3062796792941380.2365901947236070X-RAY DIFFRACTION99.9356084997
2.6925-2.86120.3280868821011400.2275975367016035X-RAY DIFFRACTION100
2.8612-3.08210.2591914947591310.2131256640716116X-RAY DIFFRACTION99.9839948784
3.0821-3.39220.2516997853831410.1891849405556090X-RAY DIFFRACTION99.9518768046
3.3922-3.88280.2036100014011430.1690133033596071X-RAY DIFFRACTION99.9678249678
3.8828-4.8910.1737809864811400.1389114621026109X-RAY DIFFRACTION99.984
4.891-46.2390.174911502211410.1813263001996154X-RAY DIFFRACTION99.5571722284

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