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- PDB-7fab: CRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINE... -

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Basic information

Entry
Database: PDB / ID: 7fab
TitleCRYSTAL STRUCTURE OF HUMAN IMMUNOGLOBULIN FRAGMENT FAB NEW REFINED AT 2.0 ANGSTROMS RESOLUTION
Components
  • IGG1-LAMBDA NEW FAB (HEAVY CHAIN)
  • IGG1-LAMBDA NEW FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / immunoglobulin complex / Initial triggering of complement / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / immune response / extracellular space / extracellular exosome / 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 C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...: / 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 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 heavy variable 4-59 / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsSaul, F. / Poljak, R.J.
Citation
Journal: Proteins / Year: 1992
Title: Crystal structure of human immunoglobulin fragment Fab New refined at 2.0 A resolution.
Authors: Saul, F.A. / Poljak, R.J.
#1: Journal: J.Biol.Chem. / Year: 1978
Title: Preliminary Refinement and Structural Analysis of the Fab Fragment from Human Immunoglobulin New at 2.0 Angstroms Resolution
Authors: Saul, F.A. / Amzel, L.M. / Poljak, R.J.
History
DepositionNov 20, 1991Processing site: BNL
SupersessionJan 31, 1994ID: 3FAB
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2013Group: Database references / Structure summary
Revision 1.4Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-LAMBDA NEW FAB (LIGHT CHAIN)
H: IGG1-LAMBDA NEW FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)45,0602
Polymers45,0602
Non-polymers00
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-19 kcal/mol
Surface area18400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.430, 56.680, 90.300
Angle α, β, γ (deg.)90.00, 116.46, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: CIS PROLINE - PRO L 137 / 2: CIS PROLINE - PRO H 151 / 3: CIS PROLINE - PRO H 153
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF THIS STRUCTURE CONTAINS TWO HOMOLOGOUS, BUT DIFFERENT, POLYPEPTIDE CHAINS WHICH ARE DESIGNATED LIGHT (L) AND HEAVY (H). COORDINATES OF WATER MOLECULES (W) ARE INCLUDED. THESE COORDINATES REPLACE A PREVIOUS ENTRY. THE STRUCTURE WAS REFINED TO 2.0 ANGSTROMS RESOLUTION WITH A MORE COMPLETE DATA SET OBTAINED BY THE USE OF AN X-RAY AREA DETECTOR.

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Components

#1: Antibody IGG1-LAMBDA NEW FAB (LIGHT CHAIN)


Mass: 22073.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P0DOY3*PLUS
#2: Antibody IGG1-LAMBDA NEW FAB (HEAVY CHAIN)


Mass: 22986.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01825*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal grow
*PLUS
Method: microdialysis
Details: referred to 'Rossi, G.', (1969) Nature., 223, 837-838
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlFab'11
20.001 MEDTA11
342 %satammonium sulfate12

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. obs: 28301 / Observed criterion σ(F): 2.5 / Num. measured all: 80611

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.169 / Rfactor obs: 0.169 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 0 229 3313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.03
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 28301 / σ(F): 2.5 / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.03

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