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- PDB-3vg0: Antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 3vg0
TitleAntibody Fab fragment
Components(Monoclonal antibody 9F8 Fab fragment ...) x 2
KeywordsIMMUNE SYSTEM / Antibody Fab fragment / Immunoglobulin fold / N-linked Glycosylation site / Fab fragment / LBD domain of ObR receptor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.27 Å
AuthorsCarpenter, B. / Hemsworth, G.R. / Ross, R.J. / Artymiuk, P.J.
CitationJournal: Structure / Year: 2012
Title: Structure of the human obesity receptor leptin-binding domain reveals the mechanism of leptin antagonism by a monoclonal antibody.
Authors: Carpenter, B. / Hemsworth, G.R. / Wu, Z. / Maamra, M. / Strasburger, C.J. / Ross, R.J. / Artymiuk, P.J.
History
DepositionJan 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
L: Monoclonal antibody 9F8 Fab fragment L chain
H: Monoclonal antibody 9F8 Fab fragment H chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4075
Polymers47,6812
Non-polymers7263
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-27 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.219, 39.966, 105.132
Angle α, β, γ (deg.)90.000, 128.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Monoclonal antibody 9F8 Fab fragment L chain


Mass: 23873.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma cell line / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody Monoclonal antibody 9F8 Fab fragment H chain


Mass: 23807.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Hybridoma cell line / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-6-deoxy-Altp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 93 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.41 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 4.6
Details: 0.2 M ammonium sulphate, 0.1 M sodium acetate pH4.6, 25% PEG-4000, vapor diffusion, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54182 Å
DetectorType: MAR345 / Detector: IMAGE PLATE / Date: May 22, 2006
RadiationMonochromator: Varimax confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.26→37.55 Å / Num. all: 21142 / Num. obs: 21142 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.3 / % possible all: 82

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1cix, chains A and D for chains L and H repectively

1cix


Resolution: 2.27→37.55 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.303 / SU ML: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.336 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1047 5.1 %RANDOM
Rwork0.19 ---
all0.1936 20419 --
obs0.1936 20419 94.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 223.4 Å2 / Biso mean: 36.8956 Å2 / Biso min: 14.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.38 Å2
2---0.14 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.27→37.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 47 91 3362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213357
X-RAY DIFFRACTIONr_angle_refined_deg1.8971.9594598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0385430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.224.215121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96315488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2741511
X-RAY DIFFRACTIONr_chiral_restr0.1230.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212514
X-RAY DIFFRACTIONr_mcbond_it9.9711.52156
X-RAY DIFFRACTIONr_mcangle_it10.35723486
X-RAY DIFFRACTIONr_scbond_it12.99131201
X-RAY DIFFRACTIONr_scangle_it13.0274.51112
LS refinement shellResolution: 2.268→2.326 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 40 -
Rwork0.251 1129 -
all-1169 -
obs--73.8 %
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)
10.9617-0.15081.09041.58880.31671.4852-0.05370.162-0.03020.0790.1723-0.0495-0.00390.0702-0.11860.1356-0.0307-0.05210.15660.02980.228664.5641.36232.92
21.69210.6381.06181.31860.43560.9348-0.01320.06820.03430.0882-0.03140.05750.00140.01910.04460.2297-0.0215-0.03010.10310.00710.155133.7188.51128.457
33.53520.91644.56740.19431.28236.77440.13780.6009-0.3294-0.04810.2564-0.0713-0.27770.6069-0.39410.16470.0135-0.0080.3657-0.08050.068761.757-4.4912.296
41.2409-1.2346-0.41561.92471.24461.2085-0.02670.23640.14640.0056-0.0383-0.0486-0.07960.12070.0650.2281-0.0116-0.00220.12920.02390.142932.36316.35314.717
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H3 - 117
2X-RAY DIFFRACTION2H118 - 221
3X-RAY DIFFRACTION3L3 - 107
4X-RAY DIFFRACTION4L108 - 215

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