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- PDB-6qf6: Structure of an E.coli expressed anti-Mcl1 scFv -

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Basic information

Entry
Database: PDB / ID: 6qf6
TitleStructure of an E.coli expressed anti-Mcl1 scFv
ComponentsE.coli expressed scFv
KeywordsAPOPTOSIS / Mcl1 / scFv / AZD5991
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLuptak, J.
CitationJournal: To Be Published
Title: Structure of an E.coli expressed anti-Mcl1 scFv
Authors: Luptak, J.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E.coli expressed scFv
B: E.coli expressed scFv
C: E.coli expressed scFv
D: E.coli expressed scFv


Theoretical massNumber of molelcules
Total (without water)102,0324
Polymers102,0324
Non-polymers00
Water4,161231
1
A: E.coli expressed scFv


Theoretical massNumber of molelcules
Total (without water)25,5081
Polymers25,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E.coli expressed scFv


Theoretical massNumber of molelcules
Total (without water)25,5081
Polymers25,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: E.coli expressed scFv


Theoretical massNumber of molelcules
Total (without water)25,5081
Polymers25,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: E.coli expressed scFv


Theoretical massNumber of molelcules
Total (without water)25,5081
Polymers25,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.175, 180.175, 88.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody
E.coli expressed scFv


Mass: 25507.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.4 M Ammonium Sulphate, 25% PEG 3350, 0.1 M BIS-TRIS pH 5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.59→127.403 Å / Num. obs: 23417 / % possible obs: 91.27 % / Redundancy: 12.92 % / Biso Wilson estimate: 42.46 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.75
Reflection shellResolution: 2.59→3.01 Å / Num. unique obs: 26817 / CC1/2: 0.369

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6qb3

6qb3


Resolution: 2.59→127.4 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.262 --RANDOM
Rwork0.181 ---
obs-23382 100 %-
Displacement parametersBiso max: 119.01 Å2 / Biso mean: 35.9746 Å2 / Biso min: 3 Å2
Refinement stepCycle: LAST / Resolution: 2.59→127.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 0 231 7034

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