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- PDB-6n2x: Anti-HIV-1 Fab 2G12 + Man9 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6n2x
TitleAnti-HIV-1 Fab 2G12 + Man9 re-refinement
Components
  • Fab 2G12 heavy chain
  • Fab 2G12 light chain
KeywordsIMMUNE SYSTEM / antibody / carbohydrate / HIV-1
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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain / Immunoglobulin kappa light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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: Science / Year: 2003
Title: Antibody domain exchange is an immunological solution to carbohydrate cluster recognition.
Authors: Calarese, D.A. / Scanlan, C.N. / Zwick, M.B. / Deechongkit, S. / Mimura, Y. / Kunert, R. / Zhu, P. / Wormald, M.R. / Stanfield, R.L. / Roux, K.H. / Kelly, J.W. / Rudd, P.M. / Dwek, R.A. / ...Authors: Calarese, D.A. / Scanlan, C.N. / Zwick, M.B. / Deechongkit, S. / Mimura, Y. / Kunert, R. / Zhu, P. / Wormald, M.R. / Stanfield, R.L. / Roux, K.H. / Kelly, J.W. / Rudd, P.M. / Dwek, R.A. / Katinger, H. / Burton, D.R. / Wilson, I.A.
History
DepositionNov 14, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionNov 28, 2018ID: 1OP5
Revision 1.0Nov 28, 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: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / pdbx_validate_symm_contact / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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
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
Revision 2.2Oct 16, 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 2G12 light chain
H: Fab 2G12 heavy chain
K: Fab 2G12 light chain
M: Fab 2G12 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9516
Polymers94,1834
Non-polymers3,7672
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint12 kcal/mol
Surface area39420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.822, 145.712, 148.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody Fab 2G12 light chain


Mass: 23245.850 Da / Num. of mol.: 2
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: 23845.791 Da / Num. of mol.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% Peg 400, 0.2M imidazole malate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.984 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3→43.3 Å / Num. obs: 29134 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 75.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 27.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1346 / % possible all: 89.9

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Processing

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

1op3
PDB Unreleased entry


Resolution: 3→43.3 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.96
RfactorNum. reflection% reflection
Rfree0.2829 1421 4.9 %
Rwork0.2433 --
obs0.2453 29009 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→43.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6581 0 254 0 6835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047012
X-RAY DIFFRACTIONf_angle_d0.9319574
X-RAY DIFFRACTIONf_dihedral_angle_d13.2074226
X-RAY DIFFRACTIONf_chiral_restr0.051153
X-RAY DIFFRACTIONf_plane_restr0.0051170
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.10730.3741300.34652653X-RAY DIFFRACTION94
3.1073-3.23160.39511540.3142733X-RAY DIFFRACTION99
3.2316-3.37870.33761380.31982779X-RAY DIFFRACTION98
3.3787-3.55670.3621340.31762768X-RAY DIFFRACTION98
3.5567-3.77940.33981740.30292705X-RAY DIFFRACTION98
3.7794-4.0710.30941400.27982748X-RAY DIFFRACTION97
4.071-4.48030.25171430.21452761X-RAY DIFFRACTION98
4.4803-5.12780.24851420.20212781X-RAY DIFFRACTION98
5.1278-6.4570.26071170.21592808X-RAY DIFFRACTION97
6.457-43.30.22661490.20032852X-RAY DIFFRACTION96

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