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- PDB-6msy: Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6msy
TitleAnti-HIV-1 Fab Fab 2G12 + Man4 re-refinement
Components
  • Fab 2G12, light chain
  • Fab 2g12, heavy chain
KeywordsIMMUNE SYSTEM / HIV-1 carbohydrate broadly neutralizing antibody / hiv neutralizing antibody / anti-carbohydrate / domain-swapping
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Immunoglobulin gamma-1 heavy chain / Immunoglobulin kappa light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsCalarese, D.A. / Stanfield, R.L. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM46192 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2005
Title: Dissection of the carbohydrate specificity of the broadly neutralizing anti-HIV-1 antibody 2G12.
Authors: Calarese, D.A. / Lee, H.K. / Huang, C.Y. / Best, M.D. / Astronomo, R.D. / Stanfield, R.L. / Katinger, H. / Burton, D.R. / Wong, C.H. / Wilson, I.A.
History
DepositionOct 18, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionNov 21, 2018ID: 1ZLS
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / 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_struct_special_symmetry / 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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab 2G12, light chain
H: Fab 2g12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9048
Polymers47,1792
Non-polymers7266
Water2,900161
1
L: Fab 2G12, light chain
H: Fab 2g12, heavy chain
hetero molecules

L: Fab 2G12, light chain
H: Fab 2g12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,80916
Polymers94,3574
Non-polymers1,45112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area12400 Å2
ΔGint-26 kcal/mol
Surface area36770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.646, 148.319, 54.604
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11L-471-

HOH

21H-414-

HOH

31H-442-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab 2G12, light chain


Mass: 23245.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX7
#2: Antibody Fab 2g12, heavy chain


Mass: 23932.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5

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Sugars , 1 types, 1 molecules

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


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1a_1-5]/1-1-1-1/a3-b1_b2-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 166 molecules

#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 3.1 Å3/Da / Density % sol: 60.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.6 / Details: 27% Peg 4000, 0.05M sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 37831 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 16.4
Reflection shellResolution: 1.99→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.35 / Num. unique obs: 1745 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OP3

1op3
PDB Unreleased entry


Resolution: 1.999→28.394 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.242 1880 4.98 %
Rwork0.206 --
obs0.2078 37772 93.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.999→28.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3209 0 53 161 3423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183348
X-RAY DIFFRACTIONf_angle_d1.5654565
X-RAY DIFFRACTIONf_dihedral_angle_d19.4941227
X-RAY DIFFRACTIONf_chiral_restr0.1532
X-RAY DIFFRACTIONf_plane_restr0.01572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9989-2.05290.33121470.2422465X-RAY DIFFRACTION86
2.0529-2.11330.29511430.24322739X-RAY DIFFRACTION94
2.1133-2.18150.26741530.23952729X-RAY DIFFRACTION94
2.1815-2.25940.25781260.25552768X-RAY DIFFRACTION95
2.2594-2.34990.29911490.23752738X-RAY DIFFRACTION95
2.3499-2.45670.27971390.22712777X-RAY DIFFRACTION95
2.4567-2.58620.29211120.22812813X-RAY DIFFRACTION95
2.5862-2.74810.27251400.22322789X-RAY DIFFRACTION96
2.7481-2.96010.23271620.23012817X-RAY DIFFRACTION97
2.9601-3.25760.29961360.21932850X-RAY DIFFRACTION96
3.2576-3.72810.23291550.20292831X-RAY DIFFRACTION96
3.7281-4.69350.20871660.17062721X-RAY DIFFRACTION91
4.6935-28.3970.20631520.18532855X-RAY DIFFRACTION92

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