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

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Basic information

Entry
Database: PDB / ID: 1lhz
TitleStructure of a Human Bence-Jones Dimer Crystallized in U.S. Space Shuttle Mission STS-95: 293K
ComponentsIMMUNOGLOBULIN LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Human Bence-Jones Dimer / Microgravity Crystallization / Induced fit
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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: 2.3 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 17, 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 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 2.2Nov 13, 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
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-18 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 85.170, 114.050
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.: 168 / 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: 2.63 Å3/Da / Density % sol: 43 %
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: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 19, 1998 / Details: Osmic multilayer
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 21524 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.6 / Num. unique all: 1943 / % possible all: 91.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 21254 / Num. measured all: 92994
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 91.7 % / Redundancy: 3 % / Num. unique obs: 1943 / Rmerge(I) obs: 0.161

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JVK

1jvk


Resolution: 2.3→25 Å / Cross valid method: R free / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target for amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2116 9.7 %Random
Rwork0.173 ---
all-21254 --
obs-21237 97.2 %-
Solvent computationBsol: 40.28 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 34.85 Å2
Baniso -1Baniso -2Baniso -3
1-6.21 Å2--
2---4.735 Å2-
3----1.477 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3154 0 0 168 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.13
X-RAY DIFFRACTIONc_angle_deg1.78
X-RAY DIFFRACTIONc_mcbond_it1.91.5
X-RAY DIFFRACTIONc_mcangle_it2.72
X-RAY DIFFRACTIONc_scbond_it3.22
X-RAY DIFFRACTIONc_scangle_it3.92.5
Refinement
*PLUS
Highest resolution: 2.3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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