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- PDB-6vrt: LT1009 humanized antibody Fab fragment in complex with calcium -

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Basic information

Entry
Database: PDB / ID: 6vrt
TitleLT1009 humanized antibody Fab fragment in complex with calcium
Components
  • Sonepcizumab antibody Fab fragment, heavy chain
  • Sonepcizumab antibody Fab fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / fab / calcium / S1P
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.555 Å
AuthorsFleming, J.K. / Huxford, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (United States)CHE-1112547 United States
CitationJournal: Antibodies / Year: 2020
Title: Ion binding properties of a naturally occurring metalloantibody
Authors: Farokhi, E. / Fleming, J.K. / Erasmus, M.F. / Ward, A.D. / Wu, Y. / Gutierrez, M.G. / Wojciak, J.M. / Huxford, T.
History
DepositionFeb 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_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.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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Sonepcizumab antibody Fab fragment, heavy chain
L: Sonepcizumab antibody Fab fragment, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0555
Polymers47,8792
Non-polymers1763
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-53 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.802, 114.408, 133.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11H-301-

SO4

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Components

#1: Antibody Sonepcizumab antibody Fab fragment, heavy chain


Mass: 24332.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Sonepcizumab antibody Fab fragment, light chain


Mass: 23546.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 uL 12 mg/mL Fab + 1 uL 0.1 M HEPES sodium, pH 7.5, 1.5 M lithium sulfate monohydrate, 10 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00008 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Sep 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00008 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 22135 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.087 / Net I/σ(I): 23.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsRsym valueDiffraction-ID% possible all
2.55-2.595.811070.771100
2.59-2.646.910870.7151100
2.64-2.697.310930.521100
2.69-2.757.410750.4571100
2.75-2.817.511060.3771100
2.81-2.877.510900.3061100
2.87-2.947.510760.2591100
2.94-3.027.511000.2321100
3.02-3.117.510840.1881100
3.11-3.217.510850.1531100
3.21-3.337.511190.131100
3.33-3.467.510880.1141100
3.46-3.627.511200.1021100
3.62-3.817.411160.0951100
3.81-4.057.510920.0941100
4.05-4.367.511070.0881100
4.36-4.87.411200.0821100
4.8-5.497.411360.0751100
5.49-6.927.311280.0631100
6.92-506.912060.034199.7

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Processing

Software
NameVersionClassification
PHENIX(1.14-3260-000)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(1.14-3260-000)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I9G

3i9g


Resolution: 2.555→48.231 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.88
RfactorNum. reflection% reflection
Rfree0.2595 1130 5.11 %
Rwork0.2088 --
obs0.2114 22124 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.555→48.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 7 28 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123452
X-RAY DIFFRACTIONf_angle_d1.1424695
X-RAY DIFFRACTIONf_dihedral_angle_d6.8762048
X-RAY DIFFRACTIONf_chiral_restr0.055527
X-RAY DIFFRACTIONf_plane_restr0.007598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5554-2.67170.46411430.35292540X-RAY DIFFRACTION97
2.6717-2.81250.4161580.33292569X-RAY DIFFRACTION100
2.8125-2.98870.38251270.29072596X-RAY DIFFRACTION100
2.9887-3.21940.33121320.29272612X-RAY DIFFRACTION100
3.2194-3.54330.34541420.24382625X-RAY DIFFRACTION100
3.5433-4.05580.26821380.20582630X-RAY DIFFRACTION100
4.0558-5.1090.19981340.1482673X-RAY DIFFRACTION100
5.109-48.23990.17881560.16992749X-RAY DIFFRACTION100

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