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- PDB-5zmj: Crystal structure of the Fab region of a neutralizing fully human... -

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Basic information

Entry
Database: PDB / ID: 5zmj
TitleCrystal structure of the Fab region of a neutralizing fully human antibody against GM-CSF
Components
  • Heavy chain of a Fab fraction of human IgG
  • Light chain of a Fab fraction of human IgG
KeywordsIMMUNE SYSTEM / Fab / fully human antibody / GM-CSF
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsAngkawidjaja, C. / Torashima, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of the Fab region of a neutralizing antibody against granulocyte-macrophage colony-stimulating factor.
Authors: Angkawidjaja, C. / Torashima, T.
History
DepositionApr 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of a Fab fraction of human IgG
L: Light chain of a Fab fraction of human IgG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,37212
Polymers51,7042
Non-polymers66810
Water8,647480
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-131 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.120, 66.690, 129.040
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 Heavy chain of a Fab fraction of human IgG


Mass: 26751.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: P01857 (UniProt) is referred. / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Light chain of a Fab fraction of human IgG


Mass: 24952.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: P0DOY2(UniProt) is referred. / Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.46 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 2.0M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→46.37 Å / Num. obs: 43756 / % possible obs: 98.1 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 27.2
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.171 / Num. unique obs: 3133

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
iMOSFLMdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EOW

4eow


Resolution: 1.81→46.37 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.006 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19133 2270 4.9 %RANDOM
Rwork0.16121 ---
obs0.16272 43716 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.529 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.81→46.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 34 480 3815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.023435
X-RAY DIFFRACTIONr_bond_other_d00.023041
X-RAY DIFFRACTIONr_angle_refined_deg0.7961.9584695
X-RAY DIFFRACTIONr_angle_other_deg0.52337108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6425444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0323.73126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40315521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0951515
X-RAY DIFFRACTIONr_chiral_restr0.0630.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.0213809
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02690
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_it2.7811.71758
X-RAY DIFFRACTIONr_mcbond_other2.7761.6991757
X-RAY DIFFRACTIONr_mcangle_it3.4622.542196
X-RAY DIFFRACTIONr_mcangle_other3.4632.5412197
X-RAY DIFFRACTIONr_scbond_it4.5972.0691677
X-RAY DIFFRACTIONr_scbond_other4.5952.0691678
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2552.9362496
X-RAY DIFFRACTIONr_long_range_B_refined7.42421.6583842
X-RAY DIFFRACTIONr_long_range_B_other7.42321.6653843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.813→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 154 -
Rwork0.167 3133 -
obs--95.22 %

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