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- PDB-8vrr: 4H11-scFv antibody -

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Basic information

Entry
Database: PDB / ID: 8vrr
Title4H11-scFv antibody
Components4H11 scFv chain
KeywordsPEPTIDE BINDING PROTEIN / IMMUNE SYSTEM / Single-chain ANTIBODY Humanized Nanobody
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLee, K. / Perry, K. / Yeku, O.O. / Spriggs, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1P01 CA190174-01A1 United States
CitationJournal: J Ovarian Res / Year: 2024
Title: Structural basis for antibody recognition of the proximal MUC16 ectodomain.
Authors: Lee, K. / Perry, K. / Xu, M. / Veillard, I. / Kumar, R. / Rao, T.D. / Rueda, B.R. / Spriggs, D.R. / Yeku, O.O.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4H11 scFv chain


Theoretical massNumber of molelcules
Total (without water)27,4491
Polymers27,4491
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.592, 112.795, 150.668
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Antibody 4H11 scFv chain


Mass: 27449.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Anti-CD34 Monoclonal Antibody scFv fragment / Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T/17 / Production host: Homo sapiens (human)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M Sodium Citrate, pH 5.0, 20% PEG 4000

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Data collection

DiffractionMean temperature: 183 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2020 / Details: KB Focussing Mirrors
RadiationMonochromator: Single Crystal Si-220 Side-Bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.36→90.3 Å / Num. obs: 18408 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 48.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.045 / Rrim(I) all: 0.083 / Χ2: 0.97 / Net I/σ(I): 15.2
Reflection shellResolution: 2.36→2.45 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.688 / Num. unique obs: 1817 / CC1/2: 0.622 / Rpim(I) all: 1.098 / Rrim(I) all: 2.021 / Χ2: 0.74 / % possible all: 94.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→75.33 Å / SU ML: 0.2937 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 35.3573
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.251 1636 10.03 %
Rwork0.2253 14682 -
obs0.2278 16318 87.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.13 Å2
Refinement stepCycle: LAST / Resolution: 2.36→75.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 0 32 1849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00971856
X-RAY DIFFRACTIONf_angle_d1.12282509
X-RAY DIFFRACTIONf_chiral_restr0.0774267
X-RAY DIFFRACTIONf_plane_restr0.0049323
X-RAY DIFFRACTIONf_dihedral_angle_d17.8649664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.430.5181080.4045910X-RAY DIFFRACTION66.93
2.43-2.510.37641090.38631025X-RAY DIFFRACTION74.8
2.51-2.60.54751190.40661054X-RAY DIFFRACTION77.73
2.6-2.70.371160.33871102X-RAY DIFFRACTION78.38
2.7-2.820.33911250.29451156X-RAY DIFFRACTION85.06
2.83-2.970.33921360.27731221X-RAY DIFFRACTION88.93
2.97-3.160.25921470.26341246X-RAY DIFFRACTION91.4
3.16-3.40.28171480.24741313X-RAY DIFFRACTION94.44
3.4-3.750.22151490.20561353X-RAY DIFFRACTION97.41
3.75-4.290.21261550.18131390X-RAY DIFFRACTION99.04
4.29-5.40.18921580.16521417X-RAY DIFFRACTION100
5.41-75.330.22281660.20811495X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: -5.43290532757 Å / Origin y: 8.85744670286 Å / Origin z: -21.8763102756 Å
111213212223313233
T0.575706329948 Å2-0.0170858360865 Å20.021815304213 Å2-0.58386806995 Å2-0.00193344346392 Å2--0.583224501066 Å2
L0.468874996956 °20.224658964208 °20.107116744452 °2-0.499062642937 °20.223637289782 °2--0.796525334724 °2
S0.0972334606824 Å °-0.038095210961 Å °0.0116330097647 Å °0.151882547581 Å °-0.00966401362541 Å °-0.0140444359168 Å °0.0401897406967 Å °-0.0481860923939 Å °0.000240099291777 Å °
Refinement TLS groupSelection details: all

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