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- PDB-1bre: IMMUNOGLOBULIN LIGHT CHAIN PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1bre
TitleIMMUNOGLOBULIN LIGHT CHAIN PROTEIN
ComponentsBENCE-JONES KAPPA I PROTEIN BRE
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsSchormann, N. / Benson, M.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Tertiary structure of an amyloid immunoglobulin light chain protein: a proposed model for amyloid fibril formation.
Authors: Schormann, N. / Murrell, J.R. / Liepnieks, J.J. / Benson, M.D.
History
DepositionJul 19, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BENCE-JONES KAPPA I PROTEIN BRE
B: BENCE-JONES KAPPA I PROTEIN BRE
C: BENCE-JONES KAPPA I PROTEIN BRE
D: BENCE-JONES KAPPA I PROTEIN BRE
E: BENCE-JONES KAPPA I PROTEIN BRE
F: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)71,6716
Polymers71,6716
Non-polymers00
Water63135
1
A: BENCE-JONES KAPPA I PROTEIN BRE
B: BENCE-JONES KAPPA I PROTEIN BRE
C: BENCE-JONES KAPPA I PROTEIN BRE
D: BENCE-JONES KAPPA I PROTEIN BRE
E: BENCE-JONES KAPPA I PROTEIN BRE
F: BENCE-JONES KAPPA I PROTEIN BRE

A: BENCE-JONES KAPPA I PROTEIN BRE
B: BENCE-JONES KAPPA I PROTEIN BRE
C: BENCE-JONES KAPPA I PROTEIN BRE
D: BENCE-JONES KAPPA I PROTEIN BRE
E: BENCE-JONES KAPPA I PROTEIN BRE
F: BENCE-JONES KAPPA I PROTEIN BRE


Theoretical massNumber of molelcules
Total (without water)143,34112
Polymers143,34112
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Unit cell
Length a, b, c (Å)82.290, 77.730, 82.200
Angle α, β, γ (deg.)90.00, 119.95, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO B 8 / 4: CIS PROLINE - PRO B 95 / 5: CIS PROLINE - PRO C 8 / 6: CIS PROLINE - PRO C 95 / 7: CIS PROLINE - PRO D 8 / 8: CIS PROLINE - PRO D 95 / 9: CIS PROLINE - PRO E 8 / 10: CIS PROLINE - PRO E 95 / 11: CIS PROLINE - PRO F 8 / 12: CIS PROLINE - PRO F 95
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.467, -0.003, 0.884), (0.004, -1, -0.002), (0.884, 0.002, 0.467)-2.46, 31.5, 1.4
2given(-0.503, -0.01, -0.864), (-0.002, -1, -0.011), (-0.864, -0.004, 0.503)61.78, 6.59, 35.28
3given(1, -0.001, 0.017), (-0.001, -1, -0.006), (0.017, 0.006, -1)-0.69, -19.97, 71.64
4given(0.489, 0.01, 0.872), (-0.007, 1, -0.008), (-0.872, -0.002, 0.489)-20.98, 13.41, 36.43
5given(-0.527, 0.019, 0.85), (0.005, 1, -0.019), (-0.85, -0.006, -0.527)0.38, 26.64, 72.57
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 B 1 .. B 107 A 1 .. A 107 0.600 MONOMER 2 TO MONOMER 1 (DIMER 1) M2 D 1 .. D 107 C 1 .. C 107 0.729 MONOMER 4 TO MONOMER 3 (DIMER 2) M3 F 1 .. F 107 E 1 .. E 107 0.658 MONOMER 6 TO MONOMER 5 (DIMER 3) M4 C 1 .. C 107 A 1 .. A 107 0.719 M4 D 1 .. D 107 B 1 .. B 107 0.761 DIMER 2 TO DIMER 1 M5 E 1 .. E 107 A 1 .. A 107 0.576 M5 F 1 .. F 107 B 1 .. B 107 0.719 DIMER 3 TO DIMER 1

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Components

#1: Antibody
BENCE-JONES KAPPA I PROTEIN BRE / BENCE-JONES


Mass: 11945.124 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: PATIENT BRE / Gene: CDNA (GENBANK ACCESSION CODE / Plasmid: PCZ11
Gene (production host): CDNA (GENBANK ACCESSION CODE U31344)
Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: PIR: I39154
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.28 %
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.25-2.5 Mammonium sulfate1reservoir
2100 mMcitrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.76→71.2 Å / Num. obs: 42843 / % possible obs: 47.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.101
Reflection
*PLUS
Observed criterion σ(I): 1 / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
R-AXISdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
X-PLOR3.1phasing
RefinementResolution: 2→5 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.337 -10 %
Rwork0.218 --
obs0.218 32373 57 %
Displacement parametersBiso mean: 16.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 0 35 5009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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