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- PDB-5l7x: Afamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II -

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Basic information

Entry
Database: PDB / ID: 5l7x
TitleAfamin antibody fragment, N14 Fab, L1- glycosylated, crystal form II
Components(Mouse Antibody Fab Fragment, IgG1-kappa ...) x 2
KeywordsIMMUNE SYSTEM / Fab / Antibody Fragment / glycosilated / Afamin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRupp, B. / Naschberger, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.
Authors: Naschberger, A. / Furnrohr, B.G. / Lenac Rovis, T. / Malic, S. / Scheffzek, K. / Dieplinger, H. / Rupp, B.
History
DepositionJun 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / 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 / _software.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Jan 10, 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
H: Mouse Antibody Fab Fragment, IgG1-kappa Heavy Chain
L: Mouse Antibody Fab Fragment, IgG1-kappa Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3178
Polymers47,3452
Non-polymers9726
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-7 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.491, 72.196, 88.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody Mouse Antibody Fab Fragment, IgG1-kappa Heavy Chain


Mass: 23686.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IgG1-kappa heavy chain, 1-214 / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody Mouse Antibody Fab Fragment, IgG1-kappa Light Chain


Mass: 23658.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IgG1-kappa light chain, 1-214 / Source: (natural) Mus musculus (house mouse)

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Sugars , 1 types, 1 molecules

#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 228 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C4H10O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.3 Å3/Da / Density % sol: 47 %
Description: Block-shaped, isotropic appearance, clear, robust
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 nL Fab (10mg/ml in 20 mM HEPES pH 7.5, 150 mM NaCl) plus 200 nL cocktail (30% PEG 1k, 200mM Ammonium Fluoride, NH4F)
Temp details: Air conditioned room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 29, 2015 / Details: Torroidal Mirror Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→44.47 Å / Num. obs: 36491 / % possible obs: 98.6 % / Redundancy: 3.9 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.8
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 1 / % possible all: 91.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
autoPROCdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IL1

1il1


Resolution: 1.86→47.06 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.149 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22794 1783 4.9 %RANDOM
Rwork0.19019 ---
obs0.19208 34797 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.381 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.28 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.86→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 64 223 3511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023422
X-RAY DIFFRACTIONr_bond_other_d0.0020.023103
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9664650
X-RAY DIFFRACTIONr_angle_other_deg0.937238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02124.574129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26115.027552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.653159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2516
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213782
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02727
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_it1.4793.6031692
X-RAY DIFFRACTIONr_mcbond_other1.4763.5971691
X-RAY DIFFRACTIONr_mcangle_it2.2626.7152114
X-RAY DIFFRACTIONr_mcangle_other2.2636.7222115
X-RAY DIFFRACTIONr_scbond_it2.4214.3281730
X-RAY DIFFRACTIONr_scbond_other2.3924.3291730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5777.7182532
X-RAY DIFFRACTIONr_long_range_B_refined6.85418.0343773
X-RAY DIFFRACTIONr_long_range_B_other6.85217.9353756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 121 -
Rwork0.373 2301 -
obs--89.64 %
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)
11.85470.00990.37632.9804-0.91782.424-0.0060.17730.1081-0.1542-0.07920.1715-0.09750.05030.08520.2441-0.0324-0.04170.1962-0.00330.0334-15.1648-14.3648-1.0109
22.8101-0.01180.58521.2104-0.15323.00090.09230.09230.0143-0.1113-0.0071-0.0171-0.05240.1753-0.08520.29280.01640.03890.22440.03950.018214.86266.3249-9.589
32.82960.2631-0.51181.7220.08671.9254-0.09720.00570.0430.1052-0.01540.10170.0013-0.05270.11260.2385-0.01930.00930.1405-0.00210.0134-7.13-11.682119.6993
42.4409-0.084-0.9572.0815-0.28333.97820.19750.30260.3496-0.10920.02080.1329-0.6085-0.2565-0.21830.30760.04670.07230.2330.03610.079710.230712.24894.6278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION1L301
3X-RAY DIFFRACTION2L108 - 213
4X-RAY DIFFRACTION3H1 - 113
5X-RAY DIFFRACTION4H114 - 214

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