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- PDB-6n35: Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6n35
TitleAnti-HIV-1 Fab 2G12 + Man1-2 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 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
2alpha-alpha-mannobiose / BENZOIC ACID / alpha-D-mannopyranose / Immunoglobulin gamma-1 heavy chain / Immunoglobulin kappa light chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 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: 1OP3
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: 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 / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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
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
K: Fab 2G12 light chain
M: Fab 2G12 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9208
Polymers94,1834
Non-polymers7374
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11150 Å2
ΔGint-44 kcal/mol
Surface area37210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.725, 94.034, 169.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules LKHM

#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

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Sugars , 2 types, 2 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 natural 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
#6: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 563 molecules

#4: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2M Sodium/Potassium Phosphate

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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: 1.747→50 Å / Num. obs: 126361 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 41.9
Reflection shellResolution: 1.747→1.78 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4479 / % possible all: 68.4

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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: 1OM3

1om3
PDB Unreleased entry


Resolution: 1.747→45.3 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.41
RfactorNum. reflection% reflection
Rfree0.2378 6387 5.07 %
Rwork0.2065 --
obs0.2081 125861 95.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.747→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 50 561 7142
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016759
X-RAY DIFFRACTIONf_angle_d1.0069205
X-RAY DIFFRACTIONf_dihedral_angle_d13.1464052
X-RAY DIFFRACTIONf_chiral_restr0.0651056
X-RAY DIFFRACTIONf_plane_restr0.0071164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7471-1.76690.32181330.28122487X-RAY DIFFRACTION60
1.7669-1.78770.33181620.27543110X-RAY DIFFRACTION75
1.7877-1.80950.29021780.27543517X-RAY DIFFRACTION83
1.8095-1.83240.28351810.26993623X-RAY DIFFRACTION88
1.8324-1.85660.31342250.27983817X-RAY DIFFRACTION92
1.8566-1.8820.3271910.27743879X-RAY DIFFRACTION93
1.882-1.90890.34592280.28853956X-RAY DIFFRACTION96
1.9089-1.93740.32122040.26544098X-RAY DIFFRACTION98
1.9374-1.96760.25032030.24074132X-RAY DIFFRACTION99
1.9676-1.99990.29192270.24174154X-RAY DIFFRACTION100
1.9999-2.03440.27892360.23574116X-RAY DIFFRACTION100
2.0344-2.07140.28472210.2444112X-RAY DIFFRACTION99
2.0714-2.11120.28672310.23964147X-RAY DIFFRACTION100
2.1112-2.15430.26552190.22584143X-RAY DIFFRACTION100
2.1543-2.20120.25362200.22694164X-RAY DIFFRACTION99
2.2012-2.25240.32330.24724088X-RAY DIFFRACTION99
2.2524-2.30870.28511910.24784172X-RAY DIFFRACTION99
2.3087-2.37110.28222490.23884110X-RAY DIFFRACTION99
2.3711-2.44090.2912330.23194161X-RAY DIFFRACTION99
2.4409-2.51960.27881970.23314162X-RAY DIFFRACTION99
2.5196-2.60970.27382120.23264180X-RAY DIFFRACTION99
2.6097-2.71420.24962320.22624133X-RAY DIFFRACTION99
2.7142-2.83770.27882500.22634123X-RAY DIFFRACTION99
2.8377-2.98730.27412210.21984141X-RAY DIFFRACTION99
2.9873-3.17440.25632260.21384166X-RAY DIFFRACTION99
3.1744-3.41940.20662160.20274158X-RAY DIFFRACTION98
3.4194-3.76330.22661950.19574177X-RAY DIFFRACTION97
3.7633-4.30750.20282330.17534105X-RAY DIFFRACTION97
4.3075-5.42560.18592290.15134079X-RAY DIFFRACTION95
5.4256-45.31550.18642110.18364064X-RAY DIFFRACTION90

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