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- PDB-2imn: Refined crystal structure of a recombinant immunoglobulin domain ... -

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Basic information

Entry
Database: PDB / ID: 2imn
TitleRefined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant
ComponentsIGA-KAPPA MCPC603 FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 1.97 Å
AuthorsSteipe, B. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant.
Authors: Steipe, B. / Pluckthun, A. / Huber, R.
History
DepositionMar 30, 1992Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_symm_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4613
Polymers12,3061
Non-polymers1552
Water2,162120
1
A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules

A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9226
Polymers24,6122
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_676x-y+1,-y+2,-z+11
Buried area1980 Å2
ΔGint-23 kcal/mol
Surface area11010 Å2
MethodPISA, PQS
2
A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules

A: IGA-KAPPA MCPC603 FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9226
Polymers24,6122
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area1170 Å2
ΔGint-40 kcal/mol
Surface area11820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.500, 86.500, 74.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Atom site foot note1: RESIDUES PRO 8 AND PRO 95 ARE CIS-PROLINES.
2: RESIDUES TYR 31, LYS 31A, LYS 103, AND ARG 108 ARE PARTIALLY DISORDERED IN THE ELECTRON DENSITY.
Components on special symmetry positions
IDModelComponents
11A-318-

SO4

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Components

#1: Antibody IGA-KAPPA MCPC603 FV (LIGHT CHAIN)


Mass: 12305.757 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208622
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
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: 3.27 Å3/Da / Density % sol: 62.41 %

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 11262 / Num. measured all: 96963 / Rmerge(I) obs: 0.086

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.149 / Highest resolution: 1.97 Å
Details: RESIDUES TYR 31, LYS 31A, LYS 103, AND ARG 108 ARE PARTIALLY DISORDERED IN THE ELECTRON DENSITY.
Refinement stepCycle: LAST / Highest resolution: 1.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms864 0 9 120 993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.015
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.23
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.97 Å / Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d / Dev ideal: 2.23

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