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- PDB-1rei: THE MOLECULAR STRUCTURE OF A DIMER COMPOSED OF THE VARIABLE PORTI... -

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Entry
Database: PDB / ID: 1rei
TitleTHE MOLECULAR STRUCTURE OF A DIMER COMPOSED OF THE VARIABLE PORTIONS OF THE BENCE-JONES PROTEIN REI REFINED AT 2.0 ANGSTROMS RESOLUTION
ComponentsBENCE-JONES PROTEIN REI (LIGHT CHAIN)Bence Jones protein
KeywordsIMMUNOGLOBULIN(PART)SEQUESTERS ANTIGENS
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / 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 / 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 / Potential therapeutics for SARS / adaptive immune response / 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 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
Immunoglobulin kappa variable 1D-33 / Immunoglobulin kappa variable 1D-33
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEpp, O. / Lattman, E.E. / Colman, P. / Fehlhammer, H. / Bode, W. / Schiffer, M. / Huber, R. / Palm, W.
Citation
Journal: Biochemistry / Year: 1975
Title: The molecular structure of a dimer composed of the variable portions of the Bence-Jones protein REI refined at 2.0-A resolution.
Authors: Epp, O. / Lattman, E.E. / Schiffer, M. / Huber, R. / Palm, W.
History
DepositionMar 17, 1976Processing site: BNL
Revision 1.0May 19, 1976Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BENCE-JONES PROTEIN REI (LIGHT CHAIN)
B: BENCE-JONES PROTEIN REI (LIGHT CHAIN)


Theoretical massNumber of molelcules
Total (without water)23,5042
Polymers23,5042
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-11 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.800, 75.800, 98.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Atom site foot note1: PROLINE A 8 HAS A CIS PEPTIDE BOND / 2: PROLINE A 95 HAS A CIS PEPTIDE BOND / 3: PROLINE B 8 HAS A CIS PEPTIDE BOND / 4: PROLINE B 95 HAS A CIS PEPTIDE BOND
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.91, -0.41511, 0.007), (-0.41396, 0.91, 0.02598), (-0.017, 0.02136, -1)
Vector: -0.2975, -0.29878, 33.146)

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Components

#1: Antibody BENCE-JONES PROTEIN REI (LIGHT CHAIN) / Bence Jones protein


Mass: 11751.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01607, UniProt: P01593*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 14993 / Num. measured all: 42464

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Processing

RefinementHighest resolution: 2 Å
Details: THE LOCAL DIAD IS NORMAL TO THE 6(1) AXIS AND INTERSECTS IT 17.05 ANGSTROMS FROM THE Z=0 PLANE IN THE +Z DIRECTION. WHEN PROJECTED ONTO THE Z=0 PLANE THE DIAD MAKES AN ANGLE OF 102.5 DEGREES ...Details: THE LOCAL DIAD IS NORMAL TO THE 6(1) AXIS AND INTERSECTS IT 17.05 ANGSTROMS FROM THE Z=0 PLANE IN THE +Z DIRECTION. WHEN PROJECTED ONTO THE Z=0 PLANE THE DIAD MAKES AN ANGLE OF 102.5 DEGREES WITH THE +X AXIS AND 17.5 DEGREES WITH THE +Y AXIS.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 53 1707
Refinement
*PLUS
Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS

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