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- PDB-5wym: Crystal structure of an anti-connexin26 scFv -

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Basic information

Entry
Database: PDB / ID: 5wym
TitleCrystal structure of an anti-connexin26 scFv
Componentsanti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain
KeywordsIMMUNE SYSTEM / antibody / scFv / connexin26
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsLi, S. / Xu, L.
CitationJournal: Front Mol Neurosci / Year: 2017
Title: Design and Characterization of a Human Monoclonal Antibody that Modulates Mutant Connexin 26 Hemichannels Implicated in Deafness and Skin Disorders
Authors: Xu, L. / Carrer, A. / Zonta, F. / Qu, Z. / Ma, P. / Li, S. / Ceriani, F. / Buratto, D. / Crispino, G. / Zorzi, V. / Ziraldo, G. / Bruno, F. / Nardin, C. / Peres, C. / Mazzarda, F. / ...Authors: Xu, L. / Carrer, A. / Zonta, F. / Qu, Z. / Ma, P. / Li, S. / Ceriani, F. / Buratto, D. / Crispino, G. / Zorzi, V. / Ziraldo, G. / Bruno, F. / Nardin, C. / Peres, C. / Mazzarda, F. / Salvatore, A.M. / Raspa, M. / Scavizzi, F. / Chu, Y. / Xie, S. / Yang, X. / Liao, J. / Liu, X. / Wang, W. / Wang, S. / Yang, G. / Lerner, R.A. / Mammano, F.
History
DepositionJan 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 1.2Nov 6, 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: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain
C: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain


Theoretical massNumber of molelcules
Total (without water)50,9292
Polymers50,9292
Non-polymers00
Water1,00956
1
A: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain

A: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain


Theoretical massNumber of molelcules
Total (without water)50,9292
Polymers50,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area3400 Å2
ΔGint-23 kcal/mol
Surface area20940 Å2
MethodPISA
2
C: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain

C: anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain


Theoretical massNumber of molelcules
Total (without water)50,9292
Polymers50,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.489, 119.489, 94.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Antibody anti-connexin26 scFv,Ig heavy chain,Linker,anti-connexin26 scFv,Ig light chain


Mass: 25464.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Production host: Mammalian expression vector pCMV-Script (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 3 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: CMOS / Date: Mar 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→50.01 Å / Num. obs: 19583 / % possible obs: 96.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.038 / Rrim(I) all: 0.108 / Χ2: 0.649 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.740.3670.0010.210.4290.44592.4
2.7-2.744.10.3140.6170.1580.3540.3691.2
2.74-2.840.2940.7180.1470.3310.37292
2.8-2.854.40.2630.9110.1230.2920.40390.4
2.85-2.924.80.2690.8420.1210.2970.39793.4
2.92-2.985.30.240.9090.1030.2630.40695.1
2.98-3.065.50.2250.9480.0960.2460.45895.2
3.06-3.145.90.2190.390.090.2380.50596.5
3.14-3.236.20.180.9750.0710.1940.49596.5
3.23-3.346.80.1460.990.0550.1560.53797.1
3.34-3.467.20.150.9870.0540.160.6297.3
3.46-3.670.1070.9930.0390.1140.65696.9
3.6-3.767.10.1040.9940.0380.1110.67896.8
3.76-3.968.10.0970.9950.0330.1030.68798.3
3.96-4.218.50.0810.9970.0270.0850.69898.9
4.21-4.538.80.070.9970.0230.0740.76599
4.53-4.998.60.0650.9980.0220.0690.73198.8
4.99-5.717.70.0650.9970.0230.0690.69298.3
5.71-7.198.60.0730.9960.0250.0780.68399

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHW

2ghw


Resolution: 2.65→50.01 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.879 / SU B: 15.227 / SU ML: 0.297 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.583 / ESU R Free: 0.315 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 947 4.8 %RANDOM
Rwork0.2356 ---
obs0.237 18623 96.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.98 Å2 / Biso mean: 40.757 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2---1.94 Å20 Å2
3---3.87 Å2
Refinement stepCycle: final / Resolution: 2.65→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 56 3570
Biso mean---21.52 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023600
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9434877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1345453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61222.338154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.84515566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4541530
X-RAY DIFFRACTIONr_chiral_restr0.0740.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212758
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 63 -
Rwork0.357 1286 -
all-1349 -
obs--91.15 %

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