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- PDB-1igm: THREE DIMENSIONAL STRUCTURE OF AN FV FROM A HUMAN IGM IMMUNOGLOBULIN -

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Basic information

Entry
Database: PDB / ID: 1igm
TitleTHREE DIMENSIONAL STRUCTURE OF AN FV FROM A HUMAN IGM IMMUNOGLOBULIN
Components
  • IGM-KAPPA POT FV (HEAVY CHAIN)
  • IGM-KAPPA POT FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsFan, Z.-C. / Guddat, L.W. / Edmundson, A.B.
CitationJournal: J.Mol.Biol. / Year: 1992
Title: Three-dimensional structure of an Fv from a human IgM immunoglobulin.
Authors: Fan, Z.C. / Shan, L. / Guddat, L.W. / He, X.M. / Gray, W.R. / Raison, R.L. / Edmundson, A.B.
History
DepositionJul 10, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGM-KAPPA POT FV (LIGHT CHAIN)
H: IGM-KAPPA POT FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)26,2602
Polymers26,2602
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area11560 Å2
MethodPISA
2
L: IGM-KAPPA POT FV (LIGHT CHAIN)
H: IGM-KAPPA POT FV (HEAVY CHAIN)

L: IGM-KAPPA POT FV (LIGHT CHAIN)
H: IGM-KAPPA POT FV (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)52,5204
Polymers52,5204
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4920 Å2
ΔGint-34 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.700, 43.700, 212.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: RESIDUES 8 AND 95 OF L CHAIN ARE CIS PROLINES.

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Components

#1: Antibody IGM-KAPPA POT FV (LIGHT CHAIN)


Mass: 12470.749 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: GenBank: 5524145
#2: Antibody IGM-KAPPA POT FV (HEAVY CHAIN)


Mass: 13789.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.93 Å3/Da / Density % sol: 36.24 %
Crystal grow
*PLUS
Temperature: 20-22 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
180 mg/mlprotein1drop
224-25 %(v/v)PEG6001reservoir
30.02 MTes1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. all: 10089 / Num. obs: 8539 / % possible obs: 84.6 % / Observed criterion σ(I): 0.5 / Num. measured all: 30357 / Rmerge(I) obs: 0.0695

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.201 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1848 0 0 147 1995
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.025
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.010.025
X-RAY DIFFRACTIONp_chiral_restr0.1350.15
X-RAY DIFFRACTIONp_singtor_nbd0.1890.3
X-RAY DIFFRACTIONp_multtor_nbd0.2380.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.170.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.53
X-RAY DIFFRACTIONp_staggered_tor23.915
X-RAY DIFFRACTIONp_orthonormal_tor26.515
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 8225 / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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