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- PDB-3oau: Antibody 2G12 Recognizes Di-Mannose Equivalently in Domain- and N... -

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Basic information

Entry
Database: PDB / ID: 3oau
TitleAntibody 2G12 Recognizes Di-Mannose Equivalently in Domain- and Non-Domain-Exchanged Forms, but only binds the HIV-1 Glycan Shield if Domain-Exchanged
Components
  • Fab 2G12, heavy chain
  • Fab 2G12, light chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2alpha-alpha-mannobiose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDoores, K.J. / Fulton, Z. / Huber, M. / Wilson, I.A. / Burton, D.R.
CitationJournal: J.Virol. / Year: 2010
Title: Antibody 2G12 recognizes di-mannose equivalently in domain- and nondomain-exchanged forms but only binds the HIV-1 glycan shield if domain exchanged.
Authors: Doores, K.J. / Fulton, Z. / Huber, M. / Wilson, I.A. / Burton, D.R.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab 2G12, heavy chain
L: Fab 2G12, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7346
Polymers47,1082
Non-polymers6274
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-45 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.301, 56.628, 57.653
Angle α, β, γ (deg.)92.91, 105.05, 92.74
Int Tables number1
Space group name H-MP1

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Fab 2G12, heavy chain


Mass: 23976.906 Da / Num. of mol.: 1 / Fragment: Fab / Mutation: I19R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#2: Antibody Fab 2G12, light chain


Mass: 23130.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 2alpha-alpha-mannobiose
DescriptorTypeProgram
DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a1122h-1a_1-5]/1-1/a2-b1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Manp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 198 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.62 Å3/Da / Density % sol: 53.08 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→19.75 Å / Num. obs: 32889 / Biso Wilson estimate: 31.64 Å2

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.75 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.8837 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 1633 5.05 %RANDOM
Rwork0.2117 ---
obs0.2134 32317 --
Displacement parametersBiso max: 132.76 Å2 / Biso mean: 46.4094 Å2 / Biso min: 22.21 Å2
Baniso -1Baniso -2Baniso -3
1-2.3161 Å2-8.0545 Å20.6111 Å2
2---8.2006 Å21.7949 Å2
3---5.8844 Å2
Refine analyzeLuzzati coordinate error obs: 0.286 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 39 195 3496
Refine LS restraints
Refine-IDTypeNumberWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d11232
X-RAY DIFFRACTIONt_trig_c_planes652
X-RAY DIFFRACTIONt_gen_planes5015
X-RAY DIFFRACTIONt_it337620
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4605
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact37214
X-RAY DIFFRACTIONt_bond_d340020.009
X-RAY DIFFRACTIONt_angle_deg463621.12
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion16.86
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2451 85 4.54 %
Rwork0.205 1787 -
all0.2067 1872 -
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)
10.4747-0.16140.15141.4791-1.22631.9450.0167-0.01440.03660.3190.06360.1095-0.5294-0.0503-0.08030.14880.00960.02660.0775-0.04330.0266-12.50168.0051-11.522
20.38590.0850.14630.5566-0.60983.5036-0.0515-0.0658-0.0207-0.06220.07160.03470.4648-0.0899-0.0201-0.0114-0.05240.00790.0025-0.0333-0.015-12.5094-8.1433-19.7634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|1 - H|137 H|144 - H|224 }H1 - 137
2X-RAY DIFFRACTION1{ H|1 - H|137 H|144 - H|224 }H144 - 224
3X-RAY DIFFRACTION2{ L|2 - L|213 }L2 - 213

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