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- PDB-2lve: RECOMBINANT LEN -

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Basic information

Entry
Database: PDB / ID: 2lve
TitleRECOMBINANT LEN
ComponentsRLEN
KeywordsIMMUNOGLOBULIN / KAPPA-IV / LIGHT CHAIN DIMER
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 LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / 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 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 / 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 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 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 4-1 / Immunoglobulin kappa variable 4-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchiffer, M. / Pokkuluri, P.R.
CitationJournal: Structure / Year: 1998
Title: A domain flip as a result of a single amino-acid substitution.
Authors: Pokkuluri, P.R. / Huang, D.B. / Raffen, R. / Cai, X. / Johnson, G. / Stevens, P.W. / Stevens, F.J. / Schiffer, M.
History
DepositionMay 13, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RLEN


Theoretical massNumber of molelcules
Total (without water)12,6501
Polymers12,6501
Non-polymers00
Water79344
1
A: RLEN

A: RLEN


Theoretical massNumber of molelcules
Total (without water)25,3002
Polymers25,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Unit cell
Length a, b, c (Å)104.400, 104.400, 58.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-220-

HOH

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Components

#1: Antibody RLEN / RECOMBINANT LEN


Mass: 12650.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: KAPPA-IV LIGHT CHAIN DIMER / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P01625, UniProt: P06312*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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 / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 68 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
230 %PEG60001drop
30.1 Msodium citrate1drop
40.2 Msodium acetate1drop
50.02 Mzinc sulfate1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.5418
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→10 Å / Num. obs: 5571 / % possible obs: 96.6 % / Observed criterion σ(I): 1 / Redundancy: 1.4 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 26
Reflection shellResolution: 2.69→2.82 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 9.2 / Rsym value: 0.346 / % possible all: 97.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVE

1lve


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.263 510 9.6 %RANDOM
Rwork0.214 ---
obs0.214 4886 92.3 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms865 0 0 44 909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.23
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it22.5
X-RAY DIFFRACTIONx_mcangle_it33.5
X-RAY DIFFRACTIONx_scbond_it23
X-RAY DIFFRACTIONx_scangle_it34
LS refinement shellResolution: 2.7→2.79 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 45 8.6 %
Rwork0.29 412 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROPARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Rfactor Rwork: 0.29

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