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- PDB-1mfa: STRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYD... -

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Basic information

Entry
Database: PDB / ID: 1mfa
TitleSTRUCTURE OF A SINGLE-CHAIN FV FRAGMENT COMPLEXED WITH A CARBOHYDRATE ANTIGEN AT 1.7 ANGSTROMS RESOLUTION
Components
  • IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
  • IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsZdanov, A. / Cygler, M.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.
Authors: Zdanov, A. / Li, Y. / Bundle, D.R. / Deng, S.J. / MacKenzie, C.R. / Narang, S.A. / Young, N.M. / Cygler, M.
#1: Journal: To be Published
Title: The Solution Structure of a Trisaccharide-Antibody Complex: Comparison of NMR Measurements with a Crystal Structure
Authors: Bundle, D.R. / Baumann, H. / Brisson, J.-R. / Gagne, S. / Zdanov, A. / Cygler, M.
#2: Journal: J.Biol.Chem. / Year: 1991
Title: Bacterial Expression and Secretion of Various Single-Chain Fv Genes Encoding Proteins Specific for a Salmonella Serotype B O-Antigen
Authors: Anand, N.N. / Mandal, S. / Mackenzie, C.R. / Sadowska, J. / Sijurskjold, B. / Young, N.M. / Budle, D.R. / Narang, S.A.
#3: Journal: Science / Year: 1991
Title: Recognition of a Cell-Surface Oligo-Saccharide of Pathogenic Salmonella by an Antibody Fab Fragment
Authors: Cygler, M. / Rose, D.R. / Bundle, D.R.
History
DepositionOct 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
H: IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9983
Polymers26,5112
Non-polymers4861
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-3 kcal/mol
Surface area10170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 61.000, 74.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)


Mass: 13310.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)


Mass: 13200.718 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Polysaccharide alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]methyl alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 486.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-2[DAbea1-3]DManp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5_1*OC][a2112h-1a_1-5][a2d12m-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Manp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-3-deoxy-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: protein solution-0.003 ml, well solution-0.0045 ml
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mMtriaccharide1drop0.0005 ml
414 %(w/v)PEG80001reservoir
550 mMTris-HCl1reservoir
60.1 M1reservoirNaCl

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Data collection

Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 22712 / % possible obs: 84.3 % / Num. measured all: 177018 / Rmerge(I) obs: 0.049

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.166 / Rfactor obs: 0.166 / Highest resolution: 1.7 Å
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 33 174 1918
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_deg2.8
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 6 Å / σ(I): 2 / Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.8

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