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- PDB-6n32: Anti-HIV-1 Fab 2G12 re-refinement -

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Basic information

Entry
Database: PDB / ID: 6n32
TitleAnti-HIV-1 Fab 2G12 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: 2.2 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: 1OM3
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 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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
M: Fab 2G12 light chain
K: Fab 2G12 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,8389
Polymers94,3574
Non-polymers4805
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-106 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.821, 94.182, 171.112
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) / 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.: 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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 3.28 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.05M ammonium sulfate, 18% Peg 6000, 0.1M 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: 0.9759 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9759 Å / Relative weight: 1
ReflectionResolution: 2.2→18.739 Å / Num. obs: 59743 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 32.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 2.96 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2672 / % possible all: 85.6

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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: 1FVD

1fvd


Resolution: 2.2→18.739 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 2890 4.85 %
Rwork0.1976 --
obs0.199 59629 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→18.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 25 277 6849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036735
X-RAY DIFFRACTIONf_angle_d0.7049171
X-RAY DIFFRACTIONf_dihedral_angle_d13.7144013
X-RAY DIFFRACTIONf_chiral_restr0.0481042
X-RAY DIFFRACTIONf_plane_restr0.0041163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1997-2.23570.29831180.24082233X-RAY DIFFRACTION79
2.2357-2.27420.3051140.24252475X-RAY DIFFRACTION87
2.2742-2.31550.25171350.24522485X-RAY DIFFRACTION87
2.3155-2.35990.23481450.23012447X-RAY DIFFRACTION87
2.3599-2.4080.24981290.22562517X-RAY DIFFRACTION88
2.408-2.46020.25641340.23432503X-RAY DIFFRACTION88
2.4602-2.51730.24071510.22982533X-RAY DIFFRACTION90
2.5173-2.58010.25911220.2312602X-RAY DIFFRACTION90
2.5801-2.64970.34691320.24422665X-RAY DIFFRACTION93
2.6497-2.72740.30211450.24722692X-RAY DIFFRACTION95
2.7274-2.81520.28631190.24472830X-RAY DIFFRACTION98
2.8152-2.91550.30211300.24532848X-RAY DIFFRACTION99
2.9155-3.03170.28691310.23592895X-RAY DIFFRACTION99
3.0317-3.16910.28371410.23382852X-RAY DIFFRACTION99
3.1691-3.33530.24551550.22152869X-RAY DIFFRACTION99
3.3353-3.54290.22521500.19962840X-RAY DIFFRACTION99
3.5429-3.81430.19881450.18752855X-RAY DIFFRACTION98
3.8143-4.19430.18941320.16662878X-RAY DIFFRACTION99
4.1943-4.79230.15721610.13592844X-RAY DIFFRACTION97
4.7923-6.00470.17361420.15842897X-RAY DIFFRACTION98
6.0047-18.73960.21541590.18172979X-RAY DIFFRACTION97

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