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- PDB-4uil: crystal structure of quinine-dependent Fab 314.1 with quinine -

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Basic information

Entry
Database: PDB / ID: 4uil
Titlecrystal structure of quinine-dependent Fab 314.1 with quinine
Components(FAB 314.1) x 2
KeywordsIMMUNE SYSTEM / FAB / QUININE-DEPENDENT / MOUSE MAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Quinine
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.853 Å
AuthorsZhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.
CitationJournal: Blood / Year: 2015
Title: Structural Basis for Quinine-Dependent Antibody Binding to Platelet Integrin Alphaiib Beta3
Authors: Zhu, J. / Zhu, J. / Bougie, D.W. / Aster, R.H. / Springer, T.A.
History
DepositionMar 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: FAB 314.1
L: FAB 314.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6273
Polymers47,3022
Non-polymers3241
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-19 kcal/mol
Surface area20130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.310, 62.310, 232.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11L-2010-

HOH

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Components

#1: Antibody FAB 314.1


Mass: 23856.650 Da / Num. of mol.: 1 / Fragment: FAB, HEAVY CHAIN, RESIDUES 1-222 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB 314.1


Mass: 23445.762 Da / Num. of mol.: 1 / Fragment: FAB, LIGHT CHAIN, RESIDUES 1-213 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#3: Chemical ChemComp-QI9 / Quinine / (3alpha,8alpha,9R)-6'-methoxycinchonan-9-ol


Mass: 324.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N2O2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.39 Å3/Da / Density % sol: 48.48 % / Description: NONE
Crystal growpH: 7
Details: 20% PEG 4000, 150 MM AMMONIUM SULFATE, AND 100 MM HEPES PH 7.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97946
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 10, 2009 / Details: DOUBLE MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 10563 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 78.12 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 6 % / Rmerge(I) obs: 0.85 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UIK

4uik


Resolution: 2.853→48.579 Å / SU ML: 0.5 / σ(F): 2 / Phase error: 40.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3352 990 9.4 %
Rwork0.2685 --
obs0.2747 10478 91.64 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 114.6 Å2
Refinement stepCycle: LAST / Resolution: 2.853→48.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 24 32 3352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033409
X-RAY DIFFRACTIONf_angle_d0.7444642
X-RAY DIFFRACTIONf_dihedral_angle_d15.2051204
X-RAY DIFFRACTIONf_chiral_restr0.03529
X-RAY DIFFRACTIONf_plane_restr0.006582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8529-3.00320.45771470.41331365X-RAY DIFFRACTION97
3.0032-3.19140.43741470.36741408X-RAY DIFFRACTION98
3.1914-3.43770.42651410.34211346X-RAY DIFFRACTION97
3.4377-3.78350.3681930.3212926X-RAY DIFFRACTION76
3.7835-4.33070.37021360.27131331X-RAY DIFFRACTION90
4.3307-5.45510.27341570.22081498X-RAY DIFFRACTION100
5.4551-48.5860.30991690.24111614X-RAY DIFFRACTION99
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)
12.6904-0.53950.04294.49971.29513.79010.4475-0.0646-0.0382-0.5593-0.2212-0.26980.01030.9109-0.29961.0127-0.00220.02381.1097-0.10470.32773.11711.3264-33.7313
21.5329-0.1357-1.47812.4472-0.57143.452-0.0601-0.6361-0.12610.62380.2398-0.3225-0.3740.8846-0.01561.1006-0.46120.09891.7633-0.26440.4274-2.693118.52451.7445
34.7752-0.2301-0.09663.04761.90338.06370.8226-0.5539-0.93341.5771-0.79370.66931.5189-0.08130.06330.9712-0.12930.00460.6938-0.20410.4942-12.0793-3.7305-28.0982
41.3134-0.5777-0.26442.0160.90275.9578-0.0829-0.33380.47610.2351-0.53650.2241-0.491-0.3066-0.42940.9786-0.53860.2551.4764-0.3826-0.0044-19.102519.8296-0.0301
52.59040.34642.57083.59473.70886.47550.4674-0.8153-0.5470.79720.21890.41670.2675-0.883-0.68251.4629-0.0786-0.02121.57380.07640.5267-3.09982.6905-44.1949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H AND RESSEQ 1:121
2X-RAY DIFFRACTION2CHAIN H AND RESSEQ 122:222
3X-RAY DIFFRACTION3CHAIN L AND RESSEQ 1:108
4X-RAY DIFFRACTION4CHAIN L AND RESSEQ 109:212
5X-RAY DIFFRACTION5CHAIN L

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