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- PDB-6qb9: Structure of an anti-Mcl1 scFv -

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Basic information

Entry
Database: PDB / ID: 6qb9
TitleStructure of an anti-Mcl1 scFv
ComponentsscFv55
KeywordsAPOPTOSIS / Mcl1 / scFv / AZD5991
Function / homologyL(+)-TARTARIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHargreaves, D.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Antibody fragments structurally enable a drug-discovery campaign on the cancer target Mcl-1.
Authors: Luptak, J. / Bista, M. / Fisher, D. / Flavell, L. / Gao, N. / Wickson, K. / Kazmirski, S.L. / Howard, T. / Rawlins, P.B. / Hargreaves, D.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
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_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: scFv55
X: scFv55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1584
Polymers52,8582
Non-polymers3002
Water3,297183
1
A: scFv55


Theoretical massNumber of molelcules
Total (without water)26,4291
Polymers26,4291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: scFv55
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7293
Polymers26,4291
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.880, 63.030, 101.700
Angle α, β, γ (deg.)90.00, 109.96, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody scFv55


Mass: 26428.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M K/Na tartrate, Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→38.9 Å / Num. obs: 39035 / % possible obs: 98.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.15 Å2 / Net I/σ(I): 8.7
Reflection shellResolution: 1.85→1.9 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→38.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.138
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1944 4.98 %RANDOM
Rwork0.2 ---
obs0.202 39035 98.5 %-
Displacement parametersBiso mean: 30.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.6277 Å20 Å20.1462 Å2
2--0.8345 Å20 Å2
3----1.4621 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.85→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 20 183 3740
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013661HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.114987HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1202SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes633HARMONIC5
X-RAY DIFFRACTIONt_it3661HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion17.57
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion476SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4107SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.86 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2854 -4.23 %
Rwork0.221 748 -
all0.2237 781 -
obs--99.35 %

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