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- PDB-4uin: crystal structure of quinine-dependent Fab 314.3 with quinine -

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Basic information

Entry
Database: PDB / ID: 4uin
Titlecrystal structure of quinine-dependent Fab 314.3 with quinine
Components(FAB 314.3) x 2
KeywordsIMMUNE SYSTEM / 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: 2.5 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 1.2Apr 19, 2017Group: Data collection
Revision 1.3Jan 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 1.4Nov 20, 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 314.3
L: FAB 314.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers47,8482
Non-polymers3241
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-21.6 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 55.460, 72.160
Angle α, β, γ (deg.)90.00, 98.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB 314.3


Mass: 24257.135 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 1-225 / Source method: isolated from a natural source / Details: ASCITES FLUID / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody FAB 314.3


Mass: 23590.900 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 1-214 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.24 Å3/Da / Density % sol: 45.04 % / Description: NONE
Crystal growpH: 7.5 / Details: 25% PEG 1500, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2012 / Details: DOUBLE MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 14747 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.11 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6

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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: 2.5→43.771 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 25.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1006 6.8 %
Rwork0.203 --
obs0.2065 14737 99.36 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 24 90 3446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043449
X-RAY DIFFRACTIONf_angle_d0.9174690
X-RAY DIFFRACTIONf_dihedral_angle_d16.3441234
X-RAY DIFFRACTIONf_chiral_restr0.032527
X-RAY DIFFRACTIONf_plane_restr0.007595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.6320.31891520.28321881X-RAY DIFFRACTION97
2.632-2.79680.3311440.27411957X-RAY DIFFRACTION100
2.7968-3.01270.32021260.24731995X-RAY DIFFRACTION100
3.0127-3.31580.27711290.23371950X-RAY DIFFRACTION100
3.3158-3.79540.26471570.20031954X-RAY DIFFRACTION100
3.7954-4.78090.20371440.15331980X-RAY DIFFRACTION99
4.7809-43.77720.19481540.15292014X-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)
11.35010.24081.32061.2973-0.1247.5509-0.02930.0641-0.0154-0.02160.04760.01010.00380.2237-0.05770.15170.0320.00830.11250.01140.2586.8127-15.2622-42.475
28.87710.237-2.39753.6325-0.89984.33870.0461-0.5735-0.18170.2080.0550.2582-0.0483-0.0621-0.05550.190.002-0.04070.180.00880.1787-11.4136-21.4221-11.2909
36.82821.6661-3.07381.3877-1.46814.5259-0.0483-0.1214-0.1841-0.04010.02050.03280.0608-0.130.02530.16960.0088-0.03040.1445-0.02960.2374-13.3079-6.0389-45.6169
45.4028-0.20213.82261.1507-0.18864.9378-0.3275-0.54220.48290.18920.0545-0.0313-0.323-0.0180.22710.24170.0291-0.0070.2983-0.07060.2865-16.5443-5.9664-9.7318
50.27420.0616-0.17970.0161-0.04340.122-0.066-0.0075-0.0682-0.0996-0.0063-0.09610.0452-0.0288-0.12220.31610.16170.07910.49110.13390.2624.807-6.8191-54.579
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 H AND RESSEQ 1226:1226

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