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- PDB-6mnf: Anti-HIV-1 Fab 2G12 + Man8 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6mnf
TitleAnti-HIV-1 Fab 2G12 + Man8 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 / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.758 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 1, 2018Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2018ID: 1ZLW
Revision 1.0Oct 31, 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 / 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 / _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

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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)95,4985
Polymers94,1834
Non-polymers1,3151
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-59 kcal/mol
Surface area38240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.210, 165.712, 169.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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) / Production host: Cricetulus griseus (Chinese hamster)
#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) / Production host: Cricetulus griseus (Chinese hamster)
#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-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose


Type: oligosaccharide / Mass: 1315.142 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,8,7/[a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-2-2-2-2-2/a3-b1_a6-e1_b2-c1_c2-d1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 4000, 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: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 33657 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.102 / Χ2: 0.929 / Net I/σ(I): 13
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 1675 / Χ2: 0.823 / % possible all: 99.6

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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: 2.758→41.071 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.14
RfactorNum. reflection% reflection
Rfree0.2516 1681 5.01 %
Rwork0.2183 --
obs0.22 33584 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.758→41.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6614 0 88 4 6706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056897
X-RAY DIFFRACTIONf_angle_d0.9699406
X-RAY DIFFRACTIONf_dihedral_angle_d14.4424160
X-RAY DIFFRACTIONf_chiral_restr0.0561094
X-RAY DIFFRACTIONf_plane_restr0.0061178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7576-2.83870.42991140.34822518X-RAY DIFFRACTION94
2.8387-2.93030.39481370.28162592X-RAY DIFFRACTION100
2.9303-3.0350.30731520.27062648X-RAY DIFFRACTION100
3.035-3.15650.35541460.27592597X-RAY DIFFRACTION100
3.1565-3.30010.26181270.25552665X-RAY DIFFRACTION100
3.3001-3.4740.26841560.23782640X-RAY DIFFRACTION100
3.474-3.69150.27041250.22062651X-RAY DIFFRACTION99
3.6915-3.97630.25031450.22552641X-RAY DIFFRACTION99
3.9763-4.37610.20371560.19072677X-RAY DIFFRACTION100
4.3761-5.00830.2011420.1682722X-RAY DIFFRACTION100
5.0083-6.30630.20521440.18922706X-RAY DIFFRACTION99
6.3063-41.07540.24231370.2042846X-RAY DIFFRACTION98

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