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- PDB-1bww: BENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT -

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Basic information

Entry
Database: PDB / ID: 1bww
TitleBENCE-JONES IMMUNOGLOBULIN REI VARIABLE PORTION, T39K MUTANT
ComponentsPROTEIN (IG KAPPA CHAIN V-I REGION REI)
KeywordsIMMUNE SYSTEM / REIV / STABILIZED IMMUNOGLOBULIN FRAGMENT / BENCE-JONES PROTEIN
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 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsUson, I. / Pohl, E. / Schneider, T.R. / Dauter, Z. / Schmidt, A. / Fritz, H.J. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: 1.7 A structure of the stabilized REIv mutant T39K. Application of local NCS restraints.
Authors: Uson, I. / Pohl, E. / Schneider, T.R. / Dauter, Z. / Schmidt, A. / Fritz, H.J. / Sheldrick, G.M.
History
DepositionSep 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (IG KAPPA CHAIN V-I REGION REI)
B: PROTEIN (IG KAPPA CHAIN V-I REGION REI)


Theoretical massNumber of molelcules
Total (without water)23,9572
Polymers23,9572
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-10 kcal/mol
Surface area10250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.400, 40.100, 43.100
Angle α, β, γ (deg.)66.90, 85.40, 73.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99977, -0.01789, 0.01212), (-0.02119, 0.70176, -0.7121), (0.00424, -0.71219, -0.70198)
Vector: -2.00585, 0.55889, 1.45528)

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Components

#1: Antibody PROTEIN (IG KAPPA CHAIN V-I REGION REI)


Mass: 11978.282 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN KAPPA LIGHT CHAIN / Mutation: T39K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Keywords: ANTIBODY / References: UniProt: P01607, UniProt: P01593*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.26 Å3/Da / Density % sol: 45 %
Crystal growpH: 7
Details: 20% PEG 8000, 100 MM HEPES PH7 10 MG/ML PROTEIN IN 50 MM PHOSPHATE PH7, pH 7.0
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
225 mMpotassium phosphate1drop
310 %PEG80001drop
450 mMHEPES1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 1995 / Details: BENT CRYSTAL
RadiationMonochromator: GE SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.7→45 Å / Num. obs: 22266 / % possible obs: 96.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 0.95 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 2.6 / % possible all: 90.1
Reflection shell
*PLUS
% possible obs: 90.1 % / Redundancy: 1.8 % / Num. unique obs: 2104

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: REI WILDTYPE 1REI

1rei


Resolution: 1.7→45 Å / Num. parameters: 7201 / Num. restraintsaints: 9275 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56 B23 (A**2) : ESTIMATED OVERALL COORDINATE ERROR. THE STRUCTURE WAS REFINED USING LOCAL NCS RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.2208 1113 5 %RANDOM
all0.1824 22266 --
obs0.1811 -96.2 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 1640 / Occupancy sum non hydrogen: 1778
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 0 92 1796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_similar_dist0.025
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.106
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.061
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 45 Å / Num. reflection obs: 16351 / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.156 / Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.027

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