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- PDB-5l9d: AFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM... -

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Basic information

Entry
Database: PDB / ID: 5l9d
TitleAFAMIN ANTIBODY FRAGMENT, N14 FAB, L1- GLYCOSYLATED, CRYSTAL FORM I, parsimonious model
Components(MOUSE ANTIBODY FAB FRAGMENT, IGG1-KAPPA ...) x 2
KeywordsIMMUNE SYSTEM / Afamin antibody / Fab fragment / IgG1-kappa / light chain glycosilation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsRupp, B. / Naschberger, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP28395-B26 Austria
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 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Data collection
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Dec 21, 2016Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.7Jan 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)48,83211
Polymers47,3452
Non-polymers1,4889
Water3,981221
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint2 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.782, 69.249, 87.803
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 / 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 / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C

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Sugars , 1 types, 1 molecules

#8: 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 , 6 types, 229 molecules

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


Mass: 194.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Polyethylene glycol


Mass: 370.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H34O9
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H14O4
#6: 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
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: K
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 43.9 %
Description: BLOCK-SHAPED CRYSTALS WITH SHARP EDGES (0.15 X 0.15 X 0.3 MM)
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 200NL FAB 10MG/ML IN 20 MM HEPES PH 7.5 REMARK 280 7.5, 150 MM NACL PLUS 200NL 30%W/V PEG 1K, 200MM KF, pH 5.8)
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 PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015 / Details: TORROIDAL FOCUSSING MIRROR
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→54.37 Å / Num. obs: 34249 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.076 / Net I/av σ(I): 10 / Net I/σ(I): 99.8
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.4 / % possible all: 97.7

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Processing

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

1il1


Resolution: 1.88→47.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 8.279 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21505 1659 4.9 %RANDOM
Rwork0.17623 ---
obs0.17819 32346 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.896 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-0 Å20 Å2
2---0.56 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.88→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 97 221 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023565
X-RAY DIFFRACTIONr_bond_other_d0.0020.023225
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.9644839
X-RAY DIFFRACTIONr_angle_other_deg0.86437538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.535.022462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01324.58131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88615.027566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.747159
X-RAY DIFFRACTIONr_chiral_restr0.080.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213948
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02763
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_it2.0765.5321764
X-RAY DIFFRACTIONr_mcbond_other2.0715.5241763
X-RAY DIFFRACTIONr_mcangle_it3.04910.312216
X-RAY DIFFRACTIONr_mcangle_other3.05110.322217
X-RAY DIFFRACTIONr_scbond_it3.0186.351801
X-RAY DIFFRACTIONr_scbond_other3.0186.3521802
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.47711.4312616
X-RAY DIFFRACTIONr_long_range_B_refined6.39226.6073898
X-RAY DIFFRACTIONr_long_range_B_other6.36426.5713885
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 122 -
Rwork0.33 2299 -
obs--96.69 %
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)
10.84110.14810.31380.22370.06010.66440.06630.0288-0.04250.1041-0.0159-0.05130.0637-0.0449-0.05040.0977-0.0184-0.04710.0510.02790.03134.29312.067322.765
20.08240.1447-0.15881.1792-0.0310.50690.0347-0.03150.0212-0.01370.031-0.0020.01770.0753-0.06570.10230.0073-0.01280.0718-0.02880.015923.406532.118632.2646
30.08690.0565-0.04970.5517-0.00730.65910.0140.04760.01570.01590.0171-0.05530.0465-0.0378-0.03110.04120.01220.00790.0933-0.01620.03296.645811.26642.2437
40.58340.04140.20280.01390.03921.02120.0275-0.0142-0.02370.0130.0269-0.0028-0.02680.0888-0.05440.07890.0194-0.00480.1114-0.0210.010729.284926.441318.9307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 107
2X-RAY DIFFRACTION1L301
3X-RAY DIFFRACTION2L108 - 213
4X-RAY DIFFRACTION3H1 - 113
5X-RAY DIFFRACTION4H114 - 214

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