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- PDB-5mvj: Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1 -

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Basic information

Entry
Database: PDB / ID: 5mvj
TitleStructure of DC8E8 Fab at pH 6.5 crystallized in space-group P1
Components
  • antibody Fab heavy chain
  • antibody kappa chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSkrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
CitationJournal: To be published
Title: Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1
Authors: Skrabana, R. / Novak, M. / Cehlar, O. / Kontsekova, E.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: antibody Fab heavy chain
L: antibody kappa chain
A: antibody Fab heavy chain
B: antibody kappa chain
C: antibody Fab heavy chain
D: antibody kappa chain
E: antibody Fab heavy chain
F: antibody kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,3429
Polymers192,3068
Non-polymers351
Water3,009167
1
H: antibody Fab heavy chain
L: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)48,0772
Polymers48,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-23 kcal/mol
Surface area19560 Å2
MethodPISA
2
A: antibody Fab heavy chain
B: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)48,0772
Polymers48,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-21 kcal/mol
Surface area19460 Å2
MethodPISA
3
C: antibody Fab heavy chain
D: antibody kappa chain


Theoretical massNumber of molelcules
Total (without water)48,0772
Polymers48,0772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-22 kcal/mol
Surface area19550 Å2
MethodPISA
4
E: antibody Fab heavy chain
F: antibody kappa chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1123
Polymers48,0772
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-29 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.220, 82.260, 89.310
Angle α, β, γ (deg.)92.320, 95.470, 89.820
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
antibody Fab heavy chain


Mass: 23800.617 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
antibody kappa chain


Mass: 24275.930 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.875
11-H, K, -L20.125
ReflectionResolution: 2.5→34.37 Å / Num. obs: 58019 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.067 % / Biso Wilson estimate: 35.944 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.113 / Χ2: 0.916 / Net I/σ(I): 9.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.562.0580.4451.9642960.6070.61496.7
2.56-2.642.0590.42.2541930.6080.55496.7
2.64-2.712.0620.3342.7640780.710.46397.1
2.71-2.82.0680.2643.4739750.790.36497.2
2.8-2.892.0750.2194.1238530.850.30297.2
2.89-2.992.0660.1784.9837210.8970.24697.6
2.99-3.12.070.1376.3535990.9380.18997.3
3.1-3.232.0680.1117.7534920.9520.15497.2
3.23-3.372.0740.099.3732680.9680.12497.4
3.37-3.542.0690.06711.8932030.9820.09397.1
3.54-3.732.070.0613.229870.9850.08396.4
3.73-3.952.0730.05514.3428100.9880.07696.5
3.95-4.232.0660.04816.0626330.9910.06695.9
4.23-4.562.0740.0418.7524830.9930.05496.3
4.56-52.0760.04118.822510.9930.05695.6
5-5.592.0720.04318.3520400.9920.05995.1
5.59-6.452.070.04915.4418060.9920.06896.1
6.45-7.912.0590.04416.215510.9950.06197.7
7.91-11.182.0530.02623.7211840.9970.03696.9
11.18-34.372.0490.02524.55960.9970.03588.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OZ4

4oz4
PDB Unreleased entry


Resolution: 2.5→34.37 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.821 / SU B: 13.624 / SU ML: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.081
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2721 2491 4.8 %RANDOM
Rwork0.2193 ---
obs0.2219 49128 86.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 107.79 Å2 / Biso mean: 32.255 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20.94 Å2-3.4 Å2
2---13.18 Å23.81 Å2
3---11.78 Å2
Refinement stepCycle: final / Resolution: 2.5→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13298 0 1 167 13466
Biso mean--39.91 20.91 -
Num. residues----1741
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213669
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212091
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.94618603
X-RAY DIFFRACTIONr_angle_other_deg1.31328267
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40451737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60924.308520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.867152186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6141548
X-RAY DIFFRACTIONr_chiral_restr0.0870.22095
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115078
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022730
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20

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