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- PDB-1lmk: THE STRUCTURE OF A BIVALENT DIABODY -

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Basic information

Entry
Database: PDB / ID: 1lmk
TitleTHE STRUCTURE OF A BIVALENT DIABODY
ComponentsANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
KeywordsIMMUNOGLOBULIN / DIABODY / SINGLE-CHAIN FV / SCFV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsWilliams, R.L.
CitationJournal: Structure / Year: 1994
Title: Crystal structure of a diabody, a bivalent antibody fragment.
Authors: Perisic, O. / Webb, P.A. / Holliger, P. / Winter, G. / Williams, R.L.
History
DepositionAug 29, 1994Processing site: BNL
Revision 1.0Mar 31, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
C: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
E: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
G: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY


Theoretical massNumber of molelcules
Total (without water)104,3124
Polymers104,3124
Non-polymers00
Water4,702261
1
A: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
C: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY


Theoretical massNumber of molelcules
Total (without water)52,1562
Polymers52,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-34 kcal/mol
Surface area19890 Å2
MethodPISA
2
E: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY
G: ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY


Theoretical massNumber of molelcules
Total (without water)52,1562
Polymers52,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-33 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.140, 80.710, 88.010
Angle α, β, γ (deg.)90.00, 99.81, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 300 / 2: CIS PROLINE - PRO C 300 / 3: CIS PROLINE - PRO E 300 / 4: CIS PROLINE - PRO G 300
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.978444, 0.000313, 0.206513), (-0.013101, -0.998079, -0.060561), (0.206097, -0.061961, 0.976568)6.24192, -11.53625, -0.81861
2given(0.973609, 0.145816, -0.175567), (0.142675, -0.989301, -0.030455), (-0.178129, 0.004602, -0.983996)7.31477, -13.098, 65.90004
3given(-0.990376, -0.138304, 0.005235), (-0.137942, 0.989455, 0.044161), (-0.011288, 0.043013, -0.999011)11.99045, -0.64938, 65.44647
4given(-0.971816, 0.015455, 0.235232), (-0.023932, -0.999161, -0.033224), (0.234522, -0.037918, 0.971371)5.76238, -11.21334, -1.82832
5given(0.965874, 0.172685, -0.193046), (0.170901, -0.984946, -0.025986), (-0.194627, -0.007892, -0.980846)7.61495, -13.78335, 65.74141
6given(-0.983136, -0.182733, 0.007162), (-0.182072, 0.981738, 0.055146), (-0.017109, 0.052912, -0.998453)11.89592, 0.36152, 65.47165
DetailsTHE MTRIX RECORDS BELOW DESCRIBE THE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE INDIVIDUAL DOMAINS IN THIS ENTRY. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES 1 A 2 - 122 C 2 - 122 2 A 2 - 122 E 2 - 122 3 A 2 - 122 G 2 - 122 4 A 201 - 312 C 201 - 312 5 A 201 - 312 E 201 - 312 6 A 201 - 312 G 210 - 312

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Components

#1: Antibody
ANTI-PHOSPHATIDYLINOSITOL SPECIFIC PHOSPHOLIPASE C DIABODY


Mass: 26078.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: L5MK16 / Plasmid: PUC-119 DERIVED GENE: L5MK16 / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA DIABODY IS A DIMER OF A SINGLE-CHAIN ANTIBODY FRAGMENT WITH A SHORT LINKER BETWEEN VH AND VL ...A DIABODY IS A DIMER OF A SINGLE-CHAIN ANTIBODY FRAGMENT WITH A SHORT LINKER BETWEEN VH AND VL DOMAINS. THE L5MK16 DIABODY IS MADE UP OF POLYPEPTIDES HAVING AN N-TERMINAL VH DOMAIN AND A C-TERMINAL VL DOMAIN. THE VH DOMAIN OF EACH CHAIN CONSISTS OF RESIDUES 1 - 122. THE VL DOMAIN OF EACH CHAIN CONSISTS OF RESIDUES 201 - 312. THE VH AND VL DOMAINS ARE CONNECTED VIA A FIVE-RESIDUE LINKER WITH THE SEQUENCE GGGGS. THE ELECTRON DENSITY FOR THE LINKER IS VISIBLE FOR CHAIN C. THE LINKERS FOR CHAINS A, E, AND G ARE INCLUDED IN THE COORDINATE ENTRY, BUT ARE NOT VISIBLE IN THE ELECTRON DENSITY. THE LINKERS FOR CHAINS A, E, AND G HAVE BEEN MODELED SO THAT THEY ARE SIMILAR IN CONFORMATION TO THE LINKER IN CHAIN C. THE LINKERS FOR EACH CHAIN ARE RESIDUES 123 - 127. THERE ARE TWO DIABODIES IN THE ASYMMETRIC UNIT OF THE CRYSTAL. CHAINS A AND C FORM ONE OF THE DIABODIES AND CHAINS E AND G FORM THE OTHER. IN SOLUTION, GEL FILTRATION SHOWS L5MK16 TO BE A DIMER. SOURCE 1 IMMUNOGLOBULIN KAPPA VH AND VL GENES JOINED BY A 5 RESIDUE LINKER.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.16 %
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
220 %(v/v)glycerol1dropprecipitant
315 %(v/v)PEG30001dropprecipitant
40.1 MTris-HCl1dropprecipitant
50.2 Msodium acetate1dropprecipitant
1protein1drop
6precipitant1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 31023 / % possible obs: 98.4 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.6 Å / Redundancy: 4 % / Num. measured all: 124443 / Rmerge(I) obs: 0.125

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.2 -
obs0.2 27844
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7352 0 0 261 7613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.4
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_d
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
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.4
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_deg

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