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- PDB-2bx5: Is FR1 the antibody's Achillies heel -

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Basic information

Entry
Database: PDB / ID: 2bx5
TitleIs FR1 the antibody's Achillies heel
ComponentsVD9 VKI LIGHT-CHAIN
KeywordsIMMUNE SYSTEM / AMYLOID / LCDD / ANTIBODY / AGGREGATION / FR1
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Myosin-reactive immunoglobulin light chain variable region
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsJames, L.C.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Beta-Edge Interactions in a Pentadecameric Human Antibody Vkappa Domain.
Authors: James, L.C. / Jones, P.C. / Mccoy, A. / Tennent, G.A. / Pepys, M.B. / Famm, K. / Winter, G.
History
DepositionJul 22, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Derived calculations / Other ...Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Jan 8, 2014Group: Source and taxonomy
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VD9 VKI LIGHT-CHAIN
B: VD9 VKI LIGHT-CHAIN
C: VD9 VKI LIGHT-CHAIN
D: VD9 VKI LIGHT-CHAIN
E: VD9 VKI LIGHT-CHAIN
F: VD9 VKI LIGHT-CHAIN
G: VD9 VKI LIGHT-CHAIN
H: VD9 VKI LIGHT-CHAIN
I: VD9 VKI LIGHT-CHAIN
J: VD9 VKI LIGHT-CHAIN
K: VD9 VKI LIGHT-CHAIN
L: VD9 VKI LIGHT-CHAIN
M: VD9 VKI LIGHT-CHAIN
N: VD9 VKI LIGHT-CHAIN
O: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)173,11115
Polymers173,11115
Non-polymers00
Water18,8801048
1
A: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
F: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
G: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
8
H: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
9
I: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
10
J: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
11
K: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
12
L: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
13
M: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
14
N: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
15
O: VD9 VKI LIGHT-CHAIN


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)191.928, 191.928, 197.439
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2015-

HOH

21E-2056-

HOH

31E-2058-

HOH

41J-2082-

HOH

51O-2060-

HOH

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Components

#1: Antibody
VD9 VKI LIGHT-CHAIN


Mass: 11540.733 Da / Num. of mol.: 15 / Fragment: LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9UL77*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1048 / 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: 2.6 Å3/Da / Density % sol: 49 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→166 Å / Num. obs: 59210 / % possible obs: 91.4 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2 / % possible all: 89.7

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HEZ

1hez


Resolution: 2.7→166 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.29 -5 %RANDOM
Rwork0.25 ---
obs0.25 59210 91 %-
Refinement stepCycle: LAST / Resolution: 2.7→166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11941 0 0 1048 12989

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