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- PDB-1lgv: Structure of a Human Bence-Jones Dimer Crystallized in U.S. Space... -

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Basic information

Entry
Database: PDB / ID: 1lgv
TitleStructure of a Human Bence-Jones Dimer Crystallized in U.S. Space Shuttle Mission STS-95: 100K
ComponentsIMMUNOGLOBULIN LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Human Bence-Jones Dimer / Microgravity Crystallization / Induced fit
Function / homology
Function and homology information


extracellular region
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTerzyan, S.S. / DeWitt, C.R. / Ramsland, P.A. / Bourne, P.C. / Edmundson, A.B.
Citation
Journal: J.MOL.RECOG. / Year: 2003
Title: Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95
Authors: Terzyan, S.S. / DeWitt, C.R. / Ramsland, P.A. / Bourne, P.C. / Edmundson, A.B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Three-dimensional structure of an immunoglobulin light-chain dimer with amyloidogenic properties.
Authors: BOURNE, P.C. / RAMSLAND, P.A. / SHAN, L. / Fan, Z.C. / DeWitt, C.R. / SHULTZ, B.B. / Terzyans, S.S. / Moomaw, C.R. / Slaughter, C.A. / Guddat, L.W. / Edmundson, A.B.
History
DepositionApr 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 19, 2014Group: Other
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN
B: IMMUNOGLOBULIN LAMBDA LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)45,2182
Polymers45,2182
Non-polymers00
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-16 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.339, 83.248, 112.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IMMUNOGLOBULIN LAMBDA LIGHT CHAIN / IG A L / IMMUNOGLOBULIN LAMBDA-CHAIN / IG A1 BUR


Mass: 22608.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6PJG0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 279 K / Method: vapor diffusion / Details: PEG 8000, VAPOR DIFFUSION, temperature 279K
Crystal grow
*PLUS
Method: unknown
Details: Alvarado, U.R., (2001) J. Crystal Growth, 223, 407.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jan 18, 2001 / Details: Osmic multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 33755 / Num. obs: 29790 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.14
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.38 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.14 / Num. unique all: 3328 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 33875 / Num. measured all: 192398
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.3 % / Num. unique obs: 3328 / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVK

1jvk


Resolution: 1.95→25 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: R free / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2226 6.6 %random
Rwork0.2 ---
all-33755 --
obs-29790 94.7 %-
Solvent computationBsol: 62.1952 Å2 / ksol: 0.328193 e/Å3
Displacement parametersBiso mean: 47.11 Å2
Baniso -1Baniso -2Baniso -3
1-4.902 Å20 Å20 Å2
2---0.701 Å20 Å2
3----4.202 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 261 3415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.93
X-RAY DIFFRACTIONc_mcbond_it2.1161.5
X-RAY DIFFRACTIONc_scbond_it2.8332
X-RAY DIFFRACTIONc_mcangle_it3.552
X-RAY DIFFRACTIONc_scangle_it4.3682.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2pca.parpca.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.95

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