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- PDB-2vxv: Crystal structure of human IgG ABT-325 Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 2vxv
TitleCrystal structure of human IgG ABT-325 Fab Fragment
Components(HUMAN IGG ABT-325) x 2
KeywordsIMMUNE SYSTEM / IL-18 / FAB / TH1/TH2 CELLS / AUTOIMMUNITY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsArgiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Unusual Water-Mediated Antigenic Recognition of the Proinflammatory Cytokine Interleukin-18.
Authors: Argiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W.
History
DepositionJul 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HUMAN IGG ABT-325
L: HUMAN IGG ABT-325
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7794
Polymers47,4662
Non-polymers3132
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-33.7 kcal/mol
Surface area24110 Å2
MethodPQS
Unit cell
Length a, b, c (Å)64.406, 74.069, 107.271
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 HUMAN IGG ABT-325


Mass: 23946.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: ABT-325 IS A RECOMBINANT HUMAN MONOCLONAL ANTIBODY, DERIVED BY IN VITRO SELECTION OF HUMAN IMMUNOGLOBULIN LIBRARIES.
Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY
#2: Antibody HUMAN IGG ABT-325


Mass: 23518.990 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: ABT-325 IS A RECOMBINANT HUMAN MONOCLONAL ANTIBODY, DERIVED BY IN VITRO SELECTION OF HUMAN IMMUNOGLOBULIN LIBRARIES.
Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#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.: 576 / 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: 54.1 % / Description: NONE
Crystal growTemperature: 277 K / pH: 10.5
Details: ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER ...Details: ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER THE RESERVOIR AT 277 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE DAY.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.000037
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2003 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000037 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 83126 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8
Reflection shellResolution: 1.49→1.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FNS

1fns


Resolution: 1.49→30.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.264 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.179 4138 5 %RANDOM
Rwork0.153 ---
obs0.155 78910 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.49→30.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3333 0 20 576 3929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223693
X-RAY DIFFRACTIONr_bond_other_d0.0010.022464
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9525076
X-RAY DIFFRACTIONr_angle_other_deg0.9033.0046054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4785496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47524.485136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57715586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2781512
X-RAY DIFFRACTIONr_chiral_restr0.0960.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024255
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02739
X-RAY DIFFRACTIONr_nbd_refined0.1970.2550
X-RAY DIFFRACTIONr_nbd_other0.1970.22488
X-RAY DIFFRACTIONr_nbtor_refined0.180.21802
X-RAY DIFFRACTIONr_nbtor_other0.0860.22067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2377
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2571.53024
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50423879
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.60131597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5334.51197
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: 1.49→1.53 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 252
Rwork0.26 5150
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)
10.67960.7570.30812.09510.56930.8282-0.04670.05320.0622-0.07320.06530.0505-0.02620.0458-0.0186-0.03030.0027-0.0089-0.02680.0185-0.01924.89118.53-0.601
21.1837-0.1917-0.0081.081-0.22471.2376-0.0208-0.0589-0.05550.00740.00780.05290.0535-0.04920.0131-0.0188-0.0016-0.0117-0.03020.0009-0.02654.632-10.7424.004
31.02310.64140.02981.5876-0.38820.74220.0773-0.05060.04850.1364-0.04420.04320.02410.008-0.03310.0118-0.0073-0.0094-0.0188-0.0062-0.048430.10711.4619.972
40.3774-0.09130.08461.33330.54281.3062-0.0067-0.0112-0.05220.0387-0.01720.03620.0096-0.0290.0239-0.027-0.0029-0.0043-0.02610.0088-0.02516.94-20.4329.121
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 114
2X-RAY DIFFRACTION2H115 - 214
3X-RAY DIFFRACTION3L1 - 108
4X-RAY DIFFRACTION4L109 - 213

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