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- PDB-4k3g: Immunoglobulin lambda variable domain L5(L89S) fluorogen activati... -

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Basic information

Entry
Database: PDB / ID: 4k3g
TitleImmunoglobulin lambda variable domain L5(L89S) fluorogen activating protein
Componentsimmunoglobulin lambda variable domain L5(L89S)
KeywordsIMMUNE SYSTEM / immunoglobulin fold / fluorescence / malachite green / o-mannosylation / Thr27
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / alpha-D-mannopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsStanfield, R.L. / Szent-Gyorgyi, C. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Malachite Green Mediates Homodimerization of Antibody VL Domains to Form a Fluorescent Ternary Complex with Singular Symmetric Interfaces.
Authors: Szent-Gyorgyi, C. / Stanfield, R.L. / Andreko, S. / Dempsey, A. / Ahmed, M. / Capek, S. / Waggoner, A.S. / Wilson, I.A. / Bruchez, M.P.
History
DepositionApr 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: immunoglobulin lambda variable domain L5(L89S)
B: immunoglobulin lambda variable domain L5(L89S)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2463
Polymers25,0652
Non-polymers1801
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-7 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.86, 54.86, 95.32
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Antibody immunoglobulin lambda variable domain L5(L89S)


Mass: 12532.741 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): YVH10
#2: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium acetate, 10% 2-methyl-2,3-pentanediol , pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.04 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.93→27.43 Å / Num. all: 21287 / Num. obs: 21287 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 23.3
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1086 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→27.43 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1094 5.15 %
Rwork0.1929 --
obs0.1948 21259 99.83 %
all-21259 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.627 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.7798 Å20 Å2-0 Å2
2--2.7798 Å2-0 Å2
3----5.5596 Å2
Refinement stepCycle: LAST / Resolution: 1.93→27.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 11 141 1763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071712
X-RAY DIFFRACTIONf_angle_d1.1932343
X-RAY DIFFRACTIONf_dihedral_angle_d12.892611
X-RAY DIFFRACTIONf_chiral_restr0.08267
X-RAY DIFFRACTIONf_plane_restr0.006302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9279-2.01560.33551410.28852522X-RAY DIFFRACTION99
2.0156-2.12190.28491290.24112499X-RAY DIFFRACTION100
2.1219-2.25480.2341420.21862502X-RAY DIFFRACTION100
2.2548-2.42880.28491210.20982530X-RAY DIFFRACTION100
2.4288-2.6730.24241410.2072525X-RAY DIFFRACTION100
2.673-3.05930.25711530.19922505X-RAY DIFFRACTION100
3.0593-3.85270.20991310.17982527X-RAY DIFFRACTION100
3.8527-27.43430.18681360.15772555X-RAY DIFFRACTION100

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