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- PDB-1f6l: VARIABLE LIGHT CHAIN DIMER OF ANTI-FERRITIN ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1f6l
TitleVARIABLE LIGHT CHAIN DIMER OF ANTI-FERRITIN ANTIBODY
ComponentsANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold / variable light chain / dimer / anti-ferritin antibody
Function / homology
Function and homology information


immunoglobulin production / regulation of complement activation / CD22 mediated BCR regulation / immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis ...immunoglobulin production / regulation of complement activation / CD22 mediated BCR regulation / immunoglobulin complex / complement activation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / leukocyte migration / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / receptor-mediated endocytosis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / 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 1-39 / Immunoglobulin kappa variable 1-39
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsNymalm, Y. / Kravchuk, Z. / Salminen, T. / Chumanevich, A.A. / Dubnovitsky, A.P. / Kankare, J. / Pentikainen, O. / Lehtonen, J. / Arosio, P. / Martsev, S. / Johnson, M.S.
CitationJournal: J.STRUCT.BIOL. / Year: 2002
Title: Antiferritin VL homodimer binds human spleen ferritin with high specificity
Authors: Nymalm, Y. / Kravchuk, Z. / Salminen, T. / Chumanevich, A.A. / Dubnovitsky, A.P. / Kankare, J. / Pentikainen, O. / Lehtonen, J. / Arosio, P. / Martsev, S. / Johnson, M.S.
History
DepositionJun 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: ANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)12,7091
Polymers12,7091
Non-polymers00
Water1448
1
L: ANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN

L: ANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)25,4182
Polymers25,4182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Unit cell
Length a, b, c (Å)52.214, 52.214, 157.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody ANTI-FERRITIN IMMUNOGLOBULIN LIGHT CHAIN


Mass: 12709.074 Da / Num. of mol.: 1 / Fragment: VARIABLE LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: SPLEEN / Plasmid: PETVL / Production host: Escherichia coli (E. coli) / References: UniProt: P01600, UniProt: P01597*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 400, ammonium sulfate, hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19-10 mg/mldomain1drop
24 %PEG4001reservoir
32.2 Mammonium sulfate1reservoir
40.1 MHEPES1reservoirpH7.2

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 19, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 3589 / Num. obs: 3445 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.323 / Num. unique all: 315 / % possible all: 90.5
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 3589 / Num. measured all: 40650
Reflection shell
*PLUS
% possible obs: 90.5 % / Mean I/σ(I) obs: 3.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.8→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 328 -RANDOM
Rwork0.191 ---
all-3553 --
obs-3335 93.9 %-
Refinement stepCycle: LAST / Resolution: 2.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 0 0 8 824
Refinement
*PLUS
Lowest resolution: 500 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.007
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.34

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