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- PDB-2f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (... -

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Basic information

Entry
Database: PDB / ID: 2f58
TitleIGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120) (MN ISOLATE)
Components
  • PROTEIN (HIV-1 GP120)
  • PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))
  • PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1-IMINO-5-PENTANONE / Ig kappa chain V-III region PC 7183
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStanfield, R.L. / Cabezas, E. / Satterthwait, A.C. / Stura, E.A. / Profy, A.T. / Wilson, I.A.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Dual conformations for the HIV-1 gp120 V3 loop in complexes with different neutralizing fabs.
Authors: Stanfield, R. / Cabezas, E. / Satterthwait, A. / Stura, E. / Profy, A. / Wilson, I.
History
DepositionOct 23, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN))
H: PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN))
P: PROTEIN (HIV-1 GP120)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5644
Polymers49,4653
Non-polymers991
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-28 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.080, 114.720, 49.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody PROTEIN (IGG1 FAB 58.2 ANTIBODY (LIGHT CHAIN)) / FAB 58.2


Mass: 23573.012 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01666*PLUS
#2: Antibody PROTEIN (IGG1 FAB 58.2 ANTIBODY (HEAVY CHAIN)) / FAB 58.2


Mass: 24864.744 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Protein/peptide PROTEIN (HIV-1 GP120) / V3 LOOP


Mass: 1027.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THIS MOLECULE WAS CHEMICALLY SYNTHESIZED
#4: Chemical ChemComp-ARN / 1-IMINO-5-PENTANONE


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growpH: 5 / Details: 16% PEG4000, 0.2M IMIDAZOLE MALATE, PH 5.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: May 15, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→24 Å / Num. obs: 12923 / % possible obs: 91.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 35.1 Å2 / Rsym value: 0.076 / Net I/σ(I): 7.5
Reflection shellResolution: 2.8→3.02 Å / Redundancy: 1.99 % / Mean I/σ(I) obs: 1 / Rsym value: 0.288 / % possible all: 82.8

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Processing

Software
NameVersionClassification
UCSD-systemdata collection
UCSD-systemdata reduction
MERLOTphasing
X-PLORmodel building
X-PLOR3.851refinement
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB 58.2 PORTION OF FAB 58.2/SER-LOOP PEPTIDE COMPLEX

Resolution: 2.8→24 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.305 615 4.8 %RANDOM
Rwork0.185 ---
obs0.185 12923 91.9 %-
Displacement parametersBiso mean: 26.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.8→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3485 0 0 1 3486
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→3.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.366 115 5 %
Rwork0.276 2172 -
obs--82.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT

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