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- PDB-5d7s: Crystal structure of MOR04357, a neutralizing anti-human GM-CSF a... -

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Basic information

Entry
Database: PDB / ID: 5d7s
TitleCrystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment
Components
  • Immunglobulin G1 Fab fragment, heavy chain
  • Immunglobulin G1 Fab fragment, light chain
KeywordsIMMUNE SYSTEM / GM-CSF / affinity maturation / phage display / cytokine / antibody / PROTEROS BIOSTRUCTURES GMBH
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2S,3S)-butane-2,3-diol
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsEylenstein, R. / Weinfurtner, D. / Steidl, S. / Boettcher, J. / Augustin, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry of Education and Research16EX1022K/L Germany
CitationJournal: Mabs / Year: 2016
Title: Molecular basis of in vitro affinity maturation and functional evolution of a neutralizing anti-human GM-CSF antibody.
Authors: Eylenstein, R. / Weinfurtner, D. / Hartle, S. / Strohner, R. / Bottcher, J. / Augustin, M. / Ostendorp, R. / Steidl, S.
History
DepositionAug 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: Immunglobulin G1 Fab fragment, light chain
H: Immunglobulin G1 Fab fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8684
Polymers47,6882
Non-polymers1802
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-20 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.823, 66.922, 156.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Immunglobulin G1 Fab fragment, light chain


Mass: 22229.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Immunglobulin G1 Fab fragment, heavy chain


Mass: 25458.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-BUD / (2S,3S)-butane-2,3-diol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: 26 % PEG3350, 0.2 M NaCl and 0.1 M Tris, pH 8.25, 10.5 mg/mL protein

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→78.33 Å / Num. obs: 36714 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.17
Reflection shellResolution: 1.88→2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.618 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→78.33 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.638 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25419 1000 2.8 %RANDOM
Rwork0.21315 ---
obs0.21431 34906 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.282 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--0.98 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.88→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 12 199 3366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223216
X-RAY DIFFRACTIONr_bond_other_d0.0010.022790
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.9534397
X-RAY DIFFRACTIONr_angle_other_deg0.73636525
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0845425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9224.505111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33915466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.791158
X-RAY DIFFRACTIONr_chiral_restr0.0720.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02623
X-RAY DIFFRACTIONr_nbd_refined0.1860.2511
X-RAY DIFFRACTIONr_nbd_other0.1880.22624
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21531
X-RAY DIFFRACTIONr_nbtor_other0.0860.21750
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3722672
X-RAY DIFFRACTIONr_mcbond_other0.6782868
X-RAY DIFFRACTIONr_mcangle_it2.92333396
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.25741352
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.29561001
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
Rfree0.346 72 -
Rwork0.28 2503 -
obs--96.73 %
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)
12.65170.3921-2.39421.3982-1.83194.9864-0.4377-0.346-1.0019-0.26490.03790.01170.81820.22650.39990.22890.05230.11530.01460.16160.309116.86-6.1045.443
21.88180.027-0.53993.86230.69021.5608-0.0132-0.06890.043-0.03570.0020.110.0519-0.08380.0113-0.14860.0082-0.0296-0.13210.0201-0.1419-5.813-2.02337.758
32.6373-1.4732-2.37971.7841.08843.42150.0358-0.03410.1031-0.1888-0.0134-0.1856-0.18220.3698-0.0223-0.0167-0.0285-0.02340.00670.0314-0.087114.17917.54810.211
41.21510.31060.07793.7007-1.04572.36760.011-0.0882-0.10810.0157-0.1003-0.23770.01380.0910.0892-0.16840.0150.0176-0.11510.0213-0.14577.9866.55237.071
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 122
2X-RAY DIFFRACTION2H123 - 218
3X-RAY DIFFRACTION3L3 - 112
4X-RAY DIFFRACTION4L113 - 207

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