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- PDB-2omn: Bence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P4(3)2... -

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Basic information

Entry
Database: PDB / ID: 2omn
TitleBence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P4(3)2(1)2 Crystal Form
ComponentsBence Jones KWR Protein - Immunoglobulin Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin Light Chain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHENOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMakino, D.L. / Larson, S.B. / McPherson, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Bence Jones KWR protein structures determined by X-ray crystallography.
Authors: Makino, D.L. / Henschen-Edman, A.H. / Larson, S.B. / McPherson, A.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / 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 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bence Jones KWR Protein - Immunoglobulin Light Chain
B: Bence Jones KWR Protein - Immunoglobulin Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7806
Polymers45,3982
Non-polymers3824
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-46 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.63, 68.63, 181.66
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Bence Jones KWR Protein - Immunoglobulin Light Chain


Mass: 22698.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: urine / Source: (natural) Homo sapiens (human) / Strain: KWR
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPH / PHENOL


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5M Ammonium Sulfate, 0.1M Tris/HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→46.88 Å / Num. all: 20595 / Num. obs: 20595 / % possible obs: 76.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 35.1 Å2 / Limit h max: 32 / Limit h min: 0 / Limit k max: 18 / Limit k min: 0 / Limit l max: 73 / Limit l min: 0 / Observed criterion F max: 229355.06 / Observed criterion F min: 0.27 / Rsym value: 0.059 / Net I/σ(I): 23.1
Reflection shellResolution: 2.08→2.16 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 394 / Rsym value: 0.336 / % possible all: 15.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCL

1dcl


Resolution: 2.2→45 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: PARAMETERS FOR PYROGLUTAMIC ACID AND PHENOL WERE OBTAINED FROM HETERO-COMPOUND INFORMATION CENTRE - UPPSALA.
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1929 9.8 %RANDOM
Rwork0.226 ---
all0.232 19702 --
obs0.232 19702 86 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 37.1035 Å2 / ksol: 0.337824 e/Å3
Displacement parametersBiso max: 132.05 Å2 / Biso mean: 58.22 Å2 / Biso min: 32.89 Å2
Baniso -1Baniso -2Baniso -3
1-5.99 Å20 Å20 Å2
2--5.99 Å20 Å2
3----11.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Luzzati d res high-2.2
Refinement stepCycle: LAST / Resolution: 2.2→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 22 98 3312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcangle_it2.416
X-RAY DIFFRACTIONc_mcbond_it1.415
X-RAY DIFFRACTIONc_scangle_it2.617
X-RAY DIFFRACTIONc_scbond_it1.81
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.038
RfactorNum. reflection% reflection
Rfree0.393 109 10.3 %
Rwork0.403 946 -
all-2229 -
obs-1055 47.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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