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- PDB-1gig: REFINED THREE-DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A MURI... -

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Basic information

Entry
Database: PDB / ID: 1gig
TitleREFINED THREE-DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A MURINE IGG1, LAMBDA ANTIBODY
Components
  • IGG1-KAPPA HC19 FAB (HEAVY CHAIN)
  • IGG1-KAPPA HC19 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBizebard, T. / Knossow, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined three-dimensional structure of the Fab fragment of a murine IgGl,lambda antibody.
Authors: Bizebard, T. / Daniels, R. / Kahn, R. / Golinelli-Pimpaneau, B. / Skehel, J.J. / Knossow, M.
History
DepositionJan 20, 1993-
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IGG1-KAPPA HC19 FAB (LIGHT CHAIN)
H: IGG1-KAPPA HC19 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,3742
Polymers46,3742
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.900, 98.900, 89.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: CIS PROLINE - PRO L 144 / 2: CIS PROLINE - PRO H 156 / 3: CIS PROLINE - PRO H 158 / 4: CIS PROLINE - PRO H 198

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Components

#1: Antibody IGG1-KAPPA HC19 FAB (LIGHT CHAIN)


Mass: 22596.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387376
#2: Antibody IGG1-KAPPA HC19 FAB (HEAVY CHAIN)


Mass: 23777.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 4096752, UniProt: Q99LC4*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 216.513-514
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlHC19 Fab fragment1drop
20.15 M1dropNaCl
30.1 %1dropNaN3
41.2 M1reservoirK2HPO4
50.1 %1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 21391 / % possible obs: 93.6 % / Num. measured all: 68753 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.42 Å / % possible obs: 86.2 % / Rmerge(I) obs: 0.155

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→7 Å / σ(F): 2 /
RfactorNum. reflection
obs0.195 20393
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 0 91 3352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0430.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.491
X-RAY DIFFRACTIONp_mcangle_it2.551.5
X-RAY DIFFRACTIONp_scbond_it1.811
X-RAY DIFFRACTIONp_scangle_it2.941.5
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.160.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor20.715
X-RAY DIFFRACTIONp_orthonormal_tor17.220
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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