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- PDB-5acm: Mcg immunoglobulin variable domain with methylene blue -

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Basic information

Entry
Database: PDB / ID: 5acm
TitleMcg immunoglobulin variable domain with methylene blue
ComponentsMCG
KeywordsIMMUNE SYSTEM / MCG / IMMUNOGLOBULIN VARIABLE DOMAIN / METHYLENE BLUE
Function / homology
Function and homology information


CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding ...CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / Immunoglobulin lambda variable 2-8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsBrumshtein, B. / Esswein, S.R. / Salwinski, L. / Phillips, M.L. / Ly, A.T. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
CitationJournal: Elife / Year: 2015
Title: Inhibition by small-molecule ligands of formation of amyloid fibrils of an immunoglobulin light chain variable domain.
Authors: Brumshtein, B. / Esswein, S.R. / Salwinski, L. / Phillips, M.L. / Ly, A.T. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.S.
History
DepositionAug 17, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCG
B: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,08410
Polymers23,1312
Non-polymers9538
Water3,747208
1
A: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2346
Polymers11,5661
Non-polymers6695
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MCG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8504
Polymers11,5661
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.220, 31.080, 73.630
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody MCG


Mass: 11565.510 Da / Num. of mol.: 2 / Fragment: IG LAMBDA CHAIN V-II REGION MGC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01709
#2: Chemical ChemComp-MBT / 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM / METHYLENE BLUE / Methylene blue


Mass: 284.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N3S / Comment: medication*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.9 Å3/Da / Density % sol: 35 % / Description: NONE
Crystal growpH: 8.5
Details: 0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.907
11-h,-k,l20.093
ReflectionResolution: 1.05→40 Å / Num. obs: 73808 / % possible obs: 89 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.05→1.08 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UNU

4unu


Resolution: 1.05→39.22 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.983 / SU B: 0.23 / SU ML: 0.006 / Cross valid method: THROUGHOUT / ESU R: 0.004 / ESU R Free: 0.004 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.12234 4102 5 %RANDOM
Rwork0.11033 ---
obs0.11092 78400 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.864 Å2
Baniso -1Baniso -2Baniso -3
1--5.54 Å20 Å2-1.58 Å2
2--5.44 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.05→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 56 208 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0460.021698
X-RAY DIFFRACTIONr_bond_other_d0.0070.021482
X-RAY DIFFRACTIONr_angle_refined_deg3.2721.9842321
X-RAY DIFFRACTIONr_angle_other_deg2.1823.0033432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7152564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97115239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.251154
X-RAY DIFFRACTIONr_chiral_restr0.2440.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0211952
X-RAY DIFFRACTIONr_gen_planes_other0.0150.02372
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0281.44875
X-RAY DIFFRACTIONr_mcbond_other2.031.44874
X-RAY DIFFRACTIONr_mcangle_it2.0522.1671090
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6421.734823
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr7.42733180
X-RAY DIFFRACTIONr_sphericity_free26.787574
X-RAY DIFFRACTIONr_sphericity_bonded8.15753281
LS refinement shellResolution: 1.049→1.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.079 315 -
Rwork0.071 5577 -
obs--96.09 %

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