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- PDB-1cqk: CRYSTAL STRUCTURE OF THE CH3 DOMAIN FROM THE MAK33 ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1cqk
TitleCRYSTAL STRUCTURE OF THE CH3 DOMAIN FROM THE MAK33 ANTIBODY
ComponentsCH3 DOMAIN OF MAK33 ANTIBODY
KeywordsIMMUNE SYSTEM / CONSTANT DOMAIN / C1-SUBSET / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsThies, M.J. / Mayer, J. / Augustine, J.G. / Frederick, C.A. / Lilie, H. / Buchner, J.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Folding and association of the antibody domain CH3: prolyl isomerization preceeds dimerization.
Authors: Thies, M.J. / Mayer, J. / Augustine, J.G. / Frederick, C.A. / Lilie, H. / Buchner, J.
History
DepositionAug 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Aug 29, 2018Group: Advisory / Data collection ...Advisory / Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / entity_src_nat / pdbx_distant_solvent_atoms
Item: _entity.src_method

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CH3 DOMAIN OF MAK33 ANTIBODY
B: CH3 DOMAIN OF MAK33 ANTIBODY


Theoretical massNumber of molelcules
Total (without water)23,0422
Polymers23,0422
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-13 kcal/mol
Surface area9970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 42.800, 50.400
Angle α, β, γ (deg.)90.00, 105.93, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer.

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Components

#1: Protein CH3 DOMAIN OF MAK33 ANTIBODY


Mass: 11520.786 Da / Num. of mol.: 2 / Fragment: CH3 DOMAIN OF MAK33 ANTIBODY / Mutation: K5A, K16L, K23L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlCH31drop
20.1 MTris-HCl1reservoir
32.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 20 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 10340 / % possible obs: 93.4 % / Observed criterion σ(F): 2 / Redundancy: 5.58 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 10.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.273 / Num. unique all: 705 / % possible all: 83.6
Reflection
*PLUS
Num. measured all: 57677
Reflection shell
*PLUS
% possible obs: 83.6 % / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 2.2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 496 -RANDOM
Rwork0.1963 ---
all-10088 --
obs-9447 92.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 0 77 1699
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.35
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg

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