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- PDB-3f58: IGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (... -

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Basic information

Entry
Database: PDB / ID: 3f58
TitleIGG1 FAB FRAGMENT (58.2) COMPLEX WITH 12-RESIDUE CYCLIC PEPTIDE (INCLUDING RESIDUES 315-324 OF HIV-1 GP120 (MN ISOLATE); H315S MUTATION
Components
  • (PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))) x 2
  • PROTEIN (CYCLIC PEPTIDE (GP120))
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / HIV-1 / GP120 / V3
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
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
Revision 1.4Sep 6, 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))
H: PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2))
P: PROTEIN (CYCLIC PEPTIDE (GP120))


Theoretical massNumber of molelcules
Total (without water)49,3433
Polymers49,3433
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-29 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.470, 115.460, 49.580
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 (IMMUNOGLOBULIN GAMMA I (58.2)) / FAB 58.2


Mass: 23501.934 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN OF FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody PROTEIN (IMMUNOGLOBULIN GAMMA I (58.2)) / FAB 58.2


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


Mass: 976.070 Da / Num. of mol.: 1 / Fragment: RESIDUES 315-324 FROM HIV-1 GP120 / Mutation: H315S / Source method: obtained synthetically
Details: 12 RESIDUE HYDRAZONE-LINKED CYCLIC PEPTIDE WAS CHEMICALLY SYNTHESIZED FROM RESIDUES 316-324 OF HIV-1 GP120 STRAIN MN.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H. ...THE FAB FRAGMENT IS NUMBERED BY THE CONVENTION OF E. KABAT (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH, BETHESDA, MD. THE PORTION OF THE PEPTIDE CORRESPONDING TO GP120 IS NUMBERED ACCORDING TO THE BH10 ISOLATE SEQUENCE (L. RATNER, W. HASELTINE, R. PATARCA, K.J. LIVAK, B. STARCICH, S.F. JOSEPHS, E.R. DORAN, J.A. RAFALSKI, E.A. WHITEHORN, K. BAUMEISTER, L. IVANOFF, S.R. PETTEWAY JR., M. L. PEARSON, J.A. LAUTENBERGER, T.S. PAPAS, J. GHRAYEB, N.T. CHANG, R.C. GALLO, F. WONG-STAAL (1985) NATURE V. 313, 277-284.) (ARN, P1; SI, P315-P316; GPGRAF, P319-P324; GGG, P10-P12))

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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: pH 5.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 %PEG40001reservoir
20.2 Mimidazole malate1reservoir
415 mg/mlFab1drop
3peptide1drop2.4 times Fab molar

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1992 / Details: SUPPER DOUBLE MIRRORS
RadiationMonochromator: SUPPER DOUBLE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→47.8 Å / Num. obs: 13951 / % possible obs: 98.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.1 Å2 / Rsym value: 0.072 / Net I/σ(I): 13.2
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.218 / % possible all: 97.7
Reflection
*PLUS
Num. measured all: 47266 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 97.7 % / Num. unique obs: 2259 / Num. measured obs: 9337 / Rmerge(I) obs: 0.218

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
MERLOTphasing
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FAB PORTION OF 1ACY

1acy


Resolution: 2.8→48 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rwork0.2 --
obs0.2 13951 98.9 %
Displacement parametersBiso mean: 28.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 0 1 3470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
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_d1.32
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→2.98 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.377 2259 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32
LS refinement shell
*PLUS
Rfactor Rwork: 0.377

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