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- PDB-5waw: FcAbVance: Increasing our knowledge of antibody structural space ... -

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Basic information

Entry
Database: PDB / ID: 5waw
TitleFcAbVance: Increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery
Components
  • fAb Heavy Chain
  • fAb Light Chain
KeywordsIMMUNE SYSTEM / fAb / AbVance project / Pistoia Alliance
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWilliams, S.P. / Reid, R.A. / Convery, M.
CitationJournal: Not Published
Title: AbVance: Increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.
Authors: Williams, S.P. / Reid, R.A. / Convery, M.A.
History
DepositionJun 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.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.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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: fAb Light Chain
H: fAb Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3677
Polymers47,0142
Non-polymers3545
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, fAb fragment of full length mAb
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-77 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.018, 58.014, 80.442
Angle α, β, γ (deg.)90.00, 124.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-302-

ZN

21H-301-

ZN

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Components

#1: Antibody fAb Light Chain


Mass: 24089.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody fAb Heavy Chain


Mass: 22923.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1m MES pH6.5, 0.01M ZnSO4, 25% v/v PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 19210 / % possible obs: 98.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.052 / Χ2: 0.865 / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-20000.95data reduction
SCALEPACK2.2.0data scaling
MOLREP11.1.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→26.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 19.38 / SU ML: 0.396 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27956 1464 7.1 %RANDOM
Rwork0.23089 ---
obs0.23431 19210 85.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.066 Å2
Baniso -1Baniso -2Baniso -3
1--6.31 Å2-0 Å2-3.07 Å2
2--15.85 Å20 Å2
3----2.76 Å2
Refinement stepCycle: 1 / Resolution: 2.25→26.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3214 0 10 47 3271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193309
X-RAY DIFFRACTIONr_bond_other_d0.0020.022880
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.9454508
X-RAY DIFFRACTIONr_angle_other_deg0.91236696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3465430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35524.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00515474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6541510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02664
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_it3.557.1471729
X-RAY DIFFRACTIONr_mcbond_other3.557.1441728
X-RAY DIFFRACTIONr_mcangle_it5.67210.7042156
X-RAY DIFFRACTIONr_mcangle_other5.67110.7072157
X-RAY DIFFRACTIONr_scbond_it3.5067.3081578
X-RAY DIFFRACTIONr_scbond_other3.5027.3081578
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5610.8562352
X-RAY DIFFRACTIONr_long_range_B_refined9.89512723
X-RAY DIFFRACTIONr_long_range_B_other9.89512722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 94 -
Rwork0.431 952 -
obs--59.13 %

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