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- PDB-3oz9: Crystal Structure of anti-gp41 Fab NC-1 -

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Basic information

Entry
Database: PDB / ID: 3oz9
TitleCrystal Structure of anti-gp41 Fab NC-1
Components
  • Fab NC-1 IgG2a heavy chain
  • Fab NC-1 kappa light chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / non-neutralizing antibody / HIV-1 gp41 6-helix bundle core
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular space / metal ion binding / 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
Ig gamma-2A chain C region, A allele / Igk protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsStanfield, R.L. / Calarese, D.A. / Jiang, S. / Wilson, I.A.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of anti-gp41 Fab NC-1
Authors: Stanfield, R.L. / Calarese, D.A. / Jiang, S. / Wilson, I.A.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 28, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity_name_com / entity_src_nat ...entity_name_com / entity_src_nat / struct_ref / struct_ref_seq
Item: _struct_ref.db_code / _struct_ref.pdbx_align_begin ..._struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab NC-1 kappa light chain
H: Fab NC-1 IgG2a heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0556
Polymers46,6872
Non-polymers3684
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-30 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.373, 61.539, 154.373
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 NC-1 kappa light chain


Mass: 23102.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L95
#2: Antibody Fab NC-1 IgG2a heavy chain / Immunoglobulin heavy chain gamma polypeptide


Mass: 23584.432 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.1 Å3/Da / Density % sol: 41.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.13M sodium citrate, 0.1M sodium borate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.965 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 31, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.6→24.4 Å / Num. all: 52849 / Num. obs: 52849 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 13.2 Å2 / Rsym value: 0.081 / Net I/σ(I): 17.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 2596 / Rsym value: 0.685 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
AMoREphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCA

1nca


Resolution: 1.6→24.38 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2682 5.08 %RANDOM
Rwork0.19 ---
all0.1922 52784 --
obs0.1922 52784 99.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.424 Å2 / ksol: 0.376 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.2514 Å20 Å20 Å2
2--2.142 Å20 Å2
3---0.1094 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 24 485 3792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063446
X-RAY DIFFRACTIONf_angle_d1.0744696
X-RAY DIFFRACTIONf_dihedral_angle_d11.2851226
X-RAY DIFFRACTIONf_chiral_restr0.072526
X-RAY DIFFRACTIONf_plane_restr0.004589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6-1.62910.41531300.340425982598100
1.6291-1.66040.39631290.31326752675100
1.6604-1.69430.3851510.302125292529100
1.6943-1.73110.33821490.277726452645100
1.7311-1.77140.37011370.258925662566100
1.7714-1.81570.29631300.233426372637100
1.8157-1.86480.24661480.218326052605100
1.8648-1.91960.2211280.195425882588100
1.9196-1.98150.25451640.19092620262099
1.9815-2.05230.23951420.17482604260499
2.0523-2.13450.18831280.16722607260799
2.1345-2.23150.23011250.16832629262999
2.2315-2.34910.2031200.18232658265899
2.3491-2.49610.22251500.19372606260699
2.4961-2.68870.21831420.19192645264599
2.6887-2.95880.23161590.18752671267199
2.9588-3.3860.22211600.178626462646100
3.386-4.26230.16921380.147927182718100
4.2623-24.38290.19561520.1582855285599

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