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- PDB-4uim: crystal structure of quinine-dependent Fab 314.3 -

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Basic information

Entry
Database: PDB / ID: 4uim
Titlecrystal structure of quinine-dependent Fab 314.3
Components(FAB 314.3) x 2
KeywordsIMMUNE SYSTEM / QUININE-DEPENDENT / MOUSE MAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.3Nov 6, 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
A: FAB 314.3
B: FAB 314.3
C: FAB 314.3
D: FAB 314.3
E: FAB 314.3
F: FAB 314.3
H: FAB 314.3
L: FAB 314.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,58410
Polymers191,3928
Non-polymers1922
Water3,495194
1
H: FAB 314.3
L: FAB 314.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9443
Polymers47,8482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-39.2 kcal/mol
Surface area20290 Å2
MethodPISA
2
A: FAB 314.3
B: FAB 314.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9443
Polymers47,8482
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-38.1 kcal/mol
Surface area20480 Å2
MethodPISA
3
E: FAB 314.3
F: FAB 314.3


Theoretical massNumber of molelcules
Total (without water)47,8482
Polymers47,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-26.1 kcal/mol
Surface area20170 Å2
MethodPISA
4
C: FAB 314.3
D: FAB 314.3


Theoretical massNumber of molelcules
Total (without water)47,8482
Polymers47,8482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26.9 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.320, 145.240, 101.490
Angle α, β, γ (deg.)90.00, 90.88, 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.: 4 / 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.: 4 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.59 Å3/Da / Density % sol: 52.55 % / Description: NONE
Crystal growpH: 5.5
Details: 40% PEG 400, 200 MM MGCL2, AND 100 MM SODIUM CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.00695
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 10, 2012 / Details: DOUBLE MIRROR
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00695 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 53487 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 37.39 Å2 / Rmerge(I) obs: 0.26 / Net I/σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.9 / % 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: 2.7→49.367 Å / SU ML: 0.43 / σ(F): 2 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 1035 1.9 %
Rwork0.2215 --
obs0.2223 53452 99.92 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.4 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13379 0 10 194 13583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513771
X-RAY DIFFRACTIONf_angle_d1.01818729
X-RAY DIFFRACTIONf_dihedral_angle_d11.5954950
X-RAY DIFFRACTIONf_chiral_restr0.0482103
X-RAY DIFFRACTIONf_plane_restr0.0072394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.84230.39141520.35917424X-RAY DIFFRACTION100
2.8423-3.02030.30721360.32697466X-RAY DIFFRACTION100
3.0203-3.25350.32751460.28517487X-RAY DIFFRACTION100
3.2535-3.58080.29051510.23947478X-RAY DIFFRACTION100
3.5808-4.09880.28621390.20477492X-RAY DIFFRACTION100
4.0988-5.16310.18031500.15457522X-RAY DIFFRACTION100
5.1631-49.3750.2031610.16927548X-RAY DIFFRACTION100
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)
15.65010.16890.87591.6610.41982.8823-0.00350.0097-0.07670.0041-0.09320.14960.08810.03750.14550.44550.0079-0.0270.36960.04480.60591.9959-23.89095.0831
24.1422-0.0345-0.11318.52623.00466.455-0.022-0.36410.4880.2269-0.1660.0871-0.616-0.30290.23470.32540.039-0.08860.42350.01530.491923.9934-2.755826.7669
32.16060.59080.34395.74723.12922.0579-0.1663-0.20310.4763-0.1016-0.0468-0.1252-0.2324-0.1780.11890.66230.0815-0.22060.4140.01620.7885-7.7103-3.96764.7813
47.4961-1.9633-0.66585.77811.17641.7149-0.1611.06571.3787-0.2298-0.0226-0.4776-0.28160.18830.10920.5256-0.0729-0.15290.57310.21170.78325.20747.617215.0668
54.0929-1.24513.68642.9368-0.62564.8672-1.0142-0.52761.04310.32090.1555-0.1987-1.3742-0.40580.62140.68670.0958-0.22920.4879-0.11790.6844-5.1929-1.718949.6594
65.621.21640.4927.5821-0.19713.6014-0.0125-0.252-0.57010.1284-0.17460.27330.1162-0.35430.22260.29220.015-0.02490.39620.07060.4222-32.4461-23.139333.8633
75.19442.55783.60745.71460.8543.39680.0704-0.5817-0.02460.0905-0.02250.20660.0271-0.5994-0.04070.36290.00280.0470.4990.06870.3158-2.0791-21.979257.9778
81.7374-0.1812.10071.7062-1.99438.60860.0749-0.0997-0.2786-0.09230.0113-0.16030.16040.1867-0.06830.3323-0.05560.0310.41330.03180.5506-21.4032-32.626728.711
96.8642-2.46562.39884.63360.5853.31480.0403-0.3567-0.44130.40640.119-0.04820.3931-0.2699-0.11360.347-0.0720.07570.3540.07770.33732.8204-26.854391.2352
104.5211-0.6295-0.41167.14212.95684.08820.07810.1609-0.5084-0.1577-0.00880.24460.7596-0.3192-0.04770.5924-0.1132-0.05240.35280.07690.44814.2332-47.555169.9503
113.6686-0.83451.13536.3744.75316.53990.49540.58460.1426-0.2848-0.1295-0.87290.01970.1848-0.35420.34270.03450.07370.48910.03450.592848.0202-33.658776.4968
126.0454-0.6546-0.43131.6931-0.13091.72140.04910.24080.3521-0.066-0.0162-0.0640.0312-0.0322-0.06030.58240.00670.00390.4033-0.02520.432217.8859-42.293555.6495
133.1212-0.96481.69022.9177-0.01984.2377-0.14340.15850.56120.17-0.0291-0.6882-0.18510.28760.14360.3134-0.04570.00480.34510.06870.521647.7001-71.886122.1042
145.2911-1.72480.17617.2841.56525.66830.01650.28220.5248-0.2469-0.03780.4209-0.4442-0.0332-0.04570.3852-0.0352-0.04390.35230.02910.55122.6923-50.52478.5957
156.2383-5.02040.89645.1232-1.00391.1103-0.2348-0.24340.04310.84040.1196-0.17080.0579-0.07920.10150.6514-0.0191-0.10790.4146-0.07470.38536.4742-64.934840.0263
162.46111.19373.1833.20870.65716.3122-0.0562-0.163-0.2043-0.0592-0.04360.40130.248-0.29190.07640.3709-0.00370.03120.3367-0.02680.64029.7933-55.683615.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN H AND RESID 1:125
2X-RAY DIFFRACTION2CHAIN H AND RESID 126:226
3X-RAY DIFFRACTION3CHAIN L AND RESID 1:111
4X-RAY DIFFRACTION4CHAIN L AND RESID 112:213
5X-RAY DIFFRACTION5CHAIN A AND RESID 1:125
6X-RAY DIFFRACTION6CHAIN A AND RESID 126:226
7X-RAY DIFFRACTION7CHAIN B AND RESID 1:111
8X-RAY DIFFRACTION8CHAIN B AND RESID 112:213
9X-RAY DIFFRACTION9CHAIN C AND RESID 1:125
10X-RAY DIFFRACTION10CHAIN C AND RESID 126:226
11X-RAY DIFFRACTION11CHAIN D AND RESID 1:111
12X-RAY DIFFRACTION12CHAIN D AND RESID 112:213
13X-RAY DIFFRACTION13CHAIN E AND RESID 1:125
14X-RAY DIFFRACTION14CHAIN E AND RESID 126:226
15X-RAY DIFFRACTION15CHAIN F AND RESID 1:111
16X-RAY DIFFRACTION16CHAIN F AND RESID 112:213

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