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- PDB-5nst: Human monoclonal antibody with a LAIR1 insertion -

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Basic information

Entry
Database: PDB / ID: 5nst
TitleHuman monoclonal antibody with a LAIR1 insertion
Components
  • Heavy Chain of antibody MGD21
  • Light Chain of antibody MGD21
KeywordsIMMUNE SYSTEM / Antibody LAIR1 insertion
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsHsieh, F.-L. / Higgins, M.K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust101020/Z/13/Z United Kingdom
CitationJournal: Elife / Year: 2017
Title: The structure of a LAIR1-containing human antibody reveals a novel mechanism of antigen recognition.
Authors: Hsieh, F.L. / Higgins, M.K.
History
DepositionApr 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
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_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Light Chain of antibody MGD21
B: Heavy Chain of antibody MGD21
C: Light Chain of antibody MGD21
D: Heavy Chain of antibody MGD21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,40610
Polymers125,5954
Non-polymers8116
Water81145
1
A: Light Chain of antibody MGD21
B: Heavy Chain of antibody MGD21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2956
Polymers62,7982
Non-polymers4974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-26 kcal/mol
Surface area25970 Å2
MethodPISA
2
C: Light Chain of antibody MGD21
D: Heavy Chain of antibody MGD21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1114
Polymers62,7982
Non-polymers3132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-26 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.823, 86.462, 103.998
Angle α, β, γ (deg.)90.00, 126.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Light Chain of antibody MGD21


Mass: 23472.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Heavy Chain of antibody MGD21


Mass: 39324.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000, 0.1M sodium citrate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.52→81.9 Å / Num. obs: 40863 / % possible obs: 99.8 % / Redundancy: 3.2 % / Biso Wilson estimate: 60.71 Å2 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGR and 3DIF

3kgr

3dif


Resolution: 2.52→81.9 Å / Cor.coef. Fo:Fc: 0.9306 / Cor.coef. Fo:Fc free: 0.9059 / SU R Cruickshank DPI: 0.586 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.521 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.304
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 1968 4.82 %RANDOM
Rwork0.2191 ---
obs0.2214 40863 99.7 %-
Displacement parametersBiso mean: 71.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.6001 Å20 Å29.8843 Å2
2--2.8563 Å20 Å2
3----5.4564 Å2
Refine analyzeLuzzati coordinate error obs: 0.551 Å
Refinement stepCycle: 1 / Resolution: 2.52→81.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 52 45 8361
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018520HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2311614HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2835SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes184HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1236HARMONIC5
X-RAY DIFFRACTIONt_it8520HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion20.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1154SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8498SEMIHARMONIC4
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3082 133 4.44 %
Rwork0.2642 2864 -
all0.2661 2997 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.13791.6088-0.14120.7011-0.20620.34940.5778-0.4785-1.04210.2683-0.4434-0.53220.2150.1103-0.1344-0.1982-0.1836-0.2593-0.25430.1552-0.0414-35.0941-52.213915.9497
23.27661.0176-0.95970.7223-0.56920.19190.2084-0.65240.01540.0063-0.08870.00590.10760.0765-0.1197-0.1691-0.2831-0.1478-0.04260.0563-0.284-58.4748-48.293424.1387
32.7281-0.3914-0.09811.79610.03430.84790.10920.45070.1086-0.2753-0.1236-0.5529-0.4404-0.09990.0144-0.16690.1721-0.0144-0.2206-0.0899-0.227-35.5598-40.6109-14.65
46.2955-1.16690.87361.3184-0.3562-0.22510.04571.1777-0.2969-0.0806-0.031-0.0861-0.14440.0521-0.0147-0.26840.2978-0.0470.0385-0.1573-0.4166-57.8117-45.3683-22.4323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - A|211 }
2X-RAY DIFFRACTION2{ B|1 - B|351 }
3X-RAY DIFFRACTION3{ C|1 - C|208 }
4X-RAY DIFFRACTION4{ D|1 - D|351 }

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