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- PDB-2omb: Bence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P3(1)2... -

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Basic information

Entry
Database: PDB / ID: 2omb
TitleBence Jones KWR Protein- Immunoglobulin Light Chain Dimer, P3(1)21 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: 2.9 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 21, 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
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS ENTRY

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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
C: Bence Jones KWR Protein - Immunoglobulin Light Chain
D: Bence Jones KWR Protein - Immunoglobulin Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,84815
Polymers90,7964
Non-polymers1,05311
Water28816
1
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)45,9728
Polymers45,3982
Non-polymers5746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-72 kcal/mol
Surface area19800 Å2
MethodPISA
2
C: Bence Jones KWR Protein - Immunoglobulin Light Chain
D: Bence Jones KWR Protein - Immunoglobulin Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8767
Polymers45,3982
Non-polymers4785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-69 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.520, 153.520, 93.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 22698.914 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: urine / Source: (natural) Homo sapiens (human) / Strain: KWR
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.52 Å3/Da / Density % sol: 65.03 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5 M Ammonium Sulfate, 0.1M Tris/HCl pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 14, 2001
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 27674 / Num. obs: 27674 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 57.9 Å2 / Limit h max: 45 / Limit h min: 0 / Limit k max: 45 / Limit k min: 0 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 699481.23 / Observed criterion F min: 0.45 / Rsym value: 0.1 / Net I/σ(I): 14.7
Reflection shellResolution: 2.9→3.02 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2825 / Rsym value: 0.469 / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
MAR345Version 1.2.11data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DCL

1dcl


Resolution: 2.9→40 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.284 1820 7 %random
Rwork0.235 ---
all0.238 26170 --
obs0.238 26170 91.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 49.0414 Å2 / ksol: 0.347328 e/Å3
Displacement parametersBiso max: 147 Å2 / Biso mean: 68.3 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å2-9.83 Å20 Å2
2--0.85 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-4.5 Å
Luzzati sigma a0.62 Å0.58 Å
Luzzati d res high-2.9
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6384 0 59 16 6459
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0078
X-RAY DIFFRACTIONx_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.99
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_mcbond_it1.41
X-RAY DIFFRACTIONc_scangle_it2.44
X-RAY DIFFRACTIONc_scbond_it1.52
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.376 167 7.2 %
Rwork0.345 2137 -
all-2841 -
obs-2303 81.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water.paramwater.top

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