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- PDB-4yhn: Dabigatran Reversal Agent -

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Basic information

Entry
Database: PDB / ID: 4yhn
TitleDabigatran Reversal Agent
Components
  • aDabi-Fab3 heavy chain
  • aDabi-Fab3 light chain
KeywordsIMMUNE SYSTEM / antibodies
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsSchiele, F. / Nar, H.
CitationJournal: Mabs / Year: 2015
Title: Structure-guided residence time optimization of a dabigatran reversal agent.
Authors: Schiele, F. / van Ryn, J. / Litzenburger, T. / Ritter, M. / Seeliger, D. / Nar, H.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aDabi-Fab3 heavy chain
B: aDabi-Fab3 light chain
F: aDabi-Fab3 heavy chain
L: aDabi-Fab3 light chain


Theoretical massNumber of molelcules
Total (without water)95,7694
Polymers95,7694
Non-polymers00
Water5,855325
1
A: aDabi-Fab3 heavy chain
B: aDabi-Fab3 light chain


Theoretical massNumber of molelcules
Total (without water)47,8842
Polymers47,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-27 kcal/mol
Surface area19110 Å2
MethodPISA
2
F: aDabi-Fab3 heavy chain
L: aDabi-Fab3 light chain


Theoretical massNumber of molelcules
Total (without water)47,8842
Polymers47,8842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-27 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.621, 56.142, 78.526
Angle α, β, γ (deg.)88.87, 84.87, 65.67
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody aDabi-Fab3 heavy chain


Mass: 23767.514 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#2: Antibody aDabi-Fab3 light chain


Mass: 24116.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM PCB buffer (pH 6) and 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.31→29.98 Å / Num. obs: 33587 / % possible obs: 89.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 39.75 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2.31→2.81 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.7 / % possible all: 89.4

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata scaling
XDSdata reduction
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C1E

1c1e


Resolution: 2.31→21.22 Å / Cor.coef. Fo:Fc: 0.9057 / Cor.coef. Fo:Fc free: 0.8782 / SU R Cruickshank DPI: 0.497 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.467 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.242
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1677 5 %RANDOM
Rwork0.1822 ---
obs0.1841 33555 88.85 %-
Displacement parametersBiso mean: 37.49 Å2
Baniso -1Baniso -2Baniso -3
1-9.6799 Å24.4728 Å2-6.042 Å2
2--4.1812 Å2-2.3831 Å2
3----13.8611 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: 1 / Resolution: 2.31→21.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6705 0 0 325 7030
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086878HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.119363HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2275SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1004HARMONIC5
X-RAY DIFFRACTIONt_it6878HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion16.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion909SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7866SEMIHARMONIC4
LS refinement shellResolution: 2.31→2.38 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2389 110 4.72 %
Rwork0.2127 2220 -
all0.214 2330 -
obs--88.85 %
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)
10.56060.07010.00571.137-0.84991.6781-0.02230.06590.0723-0.093-0.0063-0.1344-0.00770.15910.0286-0.07030.04290.0443-0.1309-0.00140.0399-3.3728-36.601816.791
21.19950.3475-0.43951.2337-0.19331.1748-0.09930.12330.0616-0.15590.06460.05710.107-0.12840.0346-0.11370.0444-0.0057-0.15910.0021-0.0669-19.7923-43.888318.2876
31.56670.2841-0.69290.5022-0.14541.98240.1037-0.2407-0.01480.11780.01890.07040.0082-0.1948-0.1226-0.08480.02720.0104-0.10660.0467-0.0127.8669-22.9394-37.8838
42.00480.8778-0.54941.109-0.57620.85930.1825-0.43620.24070.1931-0.22760.1273-0.23750.23610.0451-0.09110.0190.0391-0.1869-0.0697-0.071421.6135-11.9054-39.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ F|* }
4X-RAY DIFFRACTION4{ L|* }

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