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- PDB-4lex: Unliganded crystal structure of mAb7 -

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Basic information

Entry
Database: PDB / ID: 4lex
TitleUnliganded crystal structure of mAb7
Components
  • FAB HEAVY CHAIN
  • FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Fab fragment / anti-GCGR / Fab heavy and light chain / Antibody
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: 2.02 Å
AuthorsMurray, J.M. / Mukund, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Inhibitory mechanism of an allosteric antibody targeting the glucagon receptor.
Authors: Mukund, S. / Shang, Y. / Clarke, H.J. / Madjidi, A. / Corn, J.E. / Kates, L. / Kolumam, G. / Chiang, V. / Luis, E. / Murray, J. / Zhang, Y. / Hotzel, I. / Koth, C.M. / Allan, B.B.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Sep 20, 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 1.4Nov 6, 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
L: FAB HEAVY CHAIN
H: FAB LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)46,6332
Polymers46,6332
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-28 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.069, 84.184, 88.959
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11H-440-

HOH

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Components

#1: Antibody FAB HEAVY CHAIN


Mass: 23819.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Antibody FAB LIGHT CHAIN


Mass: 22813.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 30.0% Jeffamine ED-2001 (v/v) at 15 mg/mL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 27181 / % possible obs: 90.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.09 / Χ2: 1.041 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.02-2.0950.21927230.961192.8
2.09-2.185.20.1827051.006192.4
2.18-2.275.20.16727331.053192.4
2.27-2.395.30.14827101.023192.1
2.39-2.545.30.13127061.081191.5
2.54-2.745.30.11227191.074191.8
2.74-3.025.30.09827201.133191.4
3.02-3.455.30.08827161.038190.5
3.45-4.355.30.08227151.005189.5
4.35-505.30.06927341.033185.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FVD

1fvd


Resolution: 2.02→49.209 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.24 / Cross valid method: Random / σ(F): 1.36 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 1393 5.13 %
Rwork0.1852 --
obs0.187 27166 90.89 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.748 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 101.73 Å2 / Biso mean: 29.8885 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1-1.7216 Å20 Å2-0 Å2
2---0.1035 Å20 Å2
3----1.618 Å2
Refinement stepCycle: LAST / Resolution: 2.02→49.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 0 285 3565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063367
X-RAY DIFFRACTIONf_angle_d1.114588
X-RAY DIFFRACTIONf_chiral_restr0.086526
X-RAY DIFFRACTIONf_plane_restr0.005584
X-RAY DIFFRACTIONf_dihedral_angle_d13.6951198
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.02-2.090.23251360.18532555269192
2.09-2.17370.23051330.18092579271292
2.1737-2.27260.27021320.18332616274892
2.2726-2.39240.24681150.20252586270192
2.3924-2.54230.26071550.20042562271792
2.5423-2.73860.25321300.2052588271892
2.7386-3.01410.23741550.19122563271891
3.0141-3.45020.21821410.19162579272091
3.4502-4.34650.18551610.16552549271090
4.3465-49.22340.1961350.18092596273186
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40110.2690.09490.7530.01880.266-0.0382-0.08950.11730.07850.00720.0644-0.0528-0.02960.04550.1040.0078-0.01340.1154-0.0220.13612.072127.314128.0428
20.2690.10990.13780.6737-0.04580.5338-0.00520.010.0428-0.00920.00420.0025-0.00690.1336-0.00690.09920.0080.00180.1787-0.01080.14388.101920.346612.107
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN LL1 - 217
2X-RAY DIFFRACTION2CHAIN HH1 - 217

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