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- PDB-2vxu: Crystal structure of murine reference antibody 125-2H Fab fragment -

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Basic information

Entry
Database: PDB / ID: 2vxu
TitleCrystal structure of murine reference antibody 125-2H Fab fragment
Components(MURINE IGG 125-2H) x 2
KeywordsIMMUNE SYSTEM / FAB / IL-18 / AUTOIMMUNITY / TH1/TH2 CELLS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 / 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 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: MURINE IGG 125-2H
I: MURINE IGG 125-2H
L: MURINE IGG 125-2H
M: MURINE IGG 125-2H


Theoretical massNumber of molelcules
Total (without water)93,7724
Polymers93,7724
Non-polymers00
Water8,791488
1
H: MURINE IGG 125-2H
L: MURINE IGG 125-2H


Theoretical massNumber of molelcules
Total (without water)46,8862
Polymers46,8862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-26.1 kcal/mol
Surface area24660 Å2
MethodPQS
2
I: MURINE IGG 125-2H
M: MURINE IGG 125-2H


Theoretical massNumber of molelcules
Total (without water)46,8862
Polymers46,8862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-26.4 kcal/mol
Surface area24950 Å2
MethodPQS
Unit cell
Length a, b, c (Å)79.061, 92.490, 137.645
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.998317, -0.052668, 0.024272), (-0.051372, -0.997364, -0.051239), (0.026907, 0.049906, -0.998391)40.25486, -0.73686, -53.20919
2given(0.997173, -0.066201, 0.035532), (-0.064449, -0.996747, -0.048396), (0.03862, 0.045969, -0.998196)40.40932, -0.29462, -53.47594

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Components

#1: Antibody MURINE IGG 125-2H


Mass: 23260.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#2: Antibody MURINE IGG 125-2H


Mass: 23625.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell line: HYBRIDOMA / Production host: MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.7 Å3/Da / Density % sol: 54.3 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7.5
Details: FAB (13 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF RESERVOIR (10% POLYETHYLENEGLYCOL (PEG) 6000, 100 MM HEPES, PH 7.5, 5% 2, 4-METHYLPENTANEDIOL) AND SUSPENDED OVER THE RESERVOIR AT ...Details: FAB (13 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF RESERVOIR (10% POLYETHYLENEGLYCOL (PEG) 6000, 100 MM HEPES, PH 7.5, 5% 2, 4-METHYLPENTANEDIOL) 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: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 20, 2003 / Details: MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→17.5 Å / Num. obs: 41229 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.9
Reflection shellResolution: 2.33→2.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.9 / % possible all: 25.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FNS

1fns


Resolution: 2.36→17.42 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.916 / SU B: 13.513 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.371 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLECULE A (CHAINS H AND L) AND A CRYSTALLOGRAPHIC SYMMETRY MATE OF MOLECULE B (CHAINS I AND M) ARE RELATED BY TRANSLATIONAL PSEUDO- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MOLECULE A (CHAINS H AND L) AND A CRYSTALLOGRAPHIC SYMMETRY MATE OF MOLECULE B (CHAINS I AND M) ARE RELATED BY TRANSLATIONAL PSEUDO-SYMMETRY. MOLECULE A IS TRANSFORMED ONTO MOLECULE B_SYM BY ROTATION OF 4.4 DEGREES ABOUT AN AXIS WITH DIRECTION COSINES (-0.6574, 0.3326, 0. 6762) FOLLOWED BY TRANSLATION OF (0.7249, 46.9819, 53.2092) ANGSTROM UNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2091 5.1 %RANDOM
Rwork0.184 ---
obs0.187 39136 98.2 %-
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: 49.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.36→17.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 0 488 7076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226893
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.959411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93124.4275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.303151102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0831526
X-RAY DIFFRACTIONr_chiral_restr0.0890.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025234
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22902
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24581
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2522
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5511.54483
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90627110
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.41632795
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1894.52285
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: 2.36→2.42 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 120
Rwork0.201 2161
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)
12.6886-1.39981.36585.7158-3.77555.9209-0.06840.0984-0.0423-1.0551-0.1304-0.32671.01280.13170.19880.14380.0260.1182-0.22880.0134-0.261528.87-10.496-47.686
20.7524-0.4661-0.86532.80260.79414.37050.0553-0.0232-0.04340.1696-0.12140.0832-0.0256-0.24940.066-0.09160.0009-0.0261-0.11540.0008-0.227119.36-12.243-12.21
32.36071.2975-1.56683.9212-2.6575.29770.1343-0.1923-0.03260.6482-0.4167-0.2373-0.83180.60820.28250.1326-0.1564-0.1055-0.07510.0399-0.214568.50310.665-5.478
41.09330.12040.53392.23730.75313.9552-0.0771-0.0095-0.0305-0.01760.0655-0.0144-0.1834-0.10170.01160.02650.01110.0272-0.10970.0312-0.202259.81311.127-40.886
52.4148-1.073-0.07725.5651-1.954.94-0.2467-0.10640.19540.40380.2834-0.1454-0.7853-0.3981-0.03670.06620.0709-0.0312-0.1935-0.0049-0.261823.02212.415-41.61
62.3351-2.10241.25913.7044-1.93334.97010.03040.02170.04940.2391-0.0501-0.1487-0.52280.2580.0196-0.0173-0.0559-0.0286-0.1272-0.0115-0.247329.1-0.008-7.348
71.18780.67550.50322.8679-0.18163.2528-0.1067-0.0528-0.0926-0.0288-0.0461-0.12580.2432-0.06230.15280.038-0.00370.0386-0.0980.0417-0.175360.987-12.111-10.593
83.17522.1523-2.99853.4179-2.17376.1679-0.1242-0.1186-0.1757-0.12940.0274-0.27840.40890.44610.0968-0.00240.06490.0351-0.1143-0.0033-0.181369.276-1.786-44.926
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 113
2X-RAY DIFFRACTION2H114 - 216
3X-RAY DIFFRACTION3I1 - 113
4X-RAY DIFFRACTION4I114 - 216
5X-RAY DIFFRACTION5L1 - 107
6X-RAY DIFFRACTION6L108 - 214
7X-RAY DIFFRACTION7M1 - 107
8X-RAY DIFFRACTION8M108 - 214

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