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- PDB-6nfn: Fab fragment of anti-cocaine antibody h2E2 bound to benzoylecgonine -

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Basic information

Entry
Database: PDB / ID: 6nfn
TitleFab fragment of anti-cocaine antibody h2E2 bound to benzoylecgonine
Components
  • Fab h2E2 heavy chain
  • Fab h2E2 light chain
KeywordsIMMUNE SYSTEM / Fab-benzoylecgonine complex Fab fragment anti-cocaine antibody humanized mAb h2E2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / Chem-BCG / FORMIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsPokkuluri, P.R. / Tan, K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2.
Authors: Tan, K. / Zhou, M. / Ahrendt, A.J. / Duke, N.E.C. / Tabaja, N. / Ball, W.J. / Kirley, T.L. / Norman, A.B. / Joachimiak, A. / Schiffer, M. / Wilton, R. / Pokkuluri, P.R.
History
DepositionDec 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Oct 11, 2023Group: 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

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Assembly

Deposited unit
L: Fab h2E2 light chain
H: Fab h2E2 heavy chain
A: Fab h2E2 light chain
B: Fab h2E2 heavy chain
C: Fab h2E2 light chain
D: Fab h2E2 heavy chain
E: Fab h2E2 light chain
F: Fab h2E2 heavy chain
I: Fab h2E2 light chain
J: Fab h2E2 heavy chain
O: Fab h2E2 light chain
P: Fab h2E2 heavy chain
Q: Fab h2E2 light chain
R: Fab h2E2 heavy chain
M: Fab h2E2 light chain
N: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,00336
Polymers371,91316
Non-polymers3,09020
Water3,117173
1
L: Fab h2E2 light chain
H: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0366
Polymers46,4892
Non-polymers5474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-28 kcal/mol
Surface area18510 Å2
MethodPISA
2
A: Fab h2E2 light chain
B: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-25 kcal/mol
Surface area19150 Å2
MethodPISA
3
C: Fab h2E2 light chain
D: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-27 kcal/mol
Surface area18750 Å2
MethodPISA
4
E: Fab h2E2 light chain
F: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-29 kcal/mol
Surface area19100 Å2
MethodPISA
5
I: Fab h2E2 light chain
J: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-28 kcal/mol
Surface area19140 Å2
MethodPISA
6
O: Fab h2E2 light chain
P: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9436
Polymers46,4892
Non-polymers4534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-26 kcal/mol
Surface area18220 Å2
MethodPISA
7
Q: Fab h2E2 light chain
R: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-24 kcal/mol
Surface area19140 Å2
MethodPISA
8
M: Fab h2E2 light chain
N: Fab h2E2 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8374
Polymers46,4892
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-34 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.049, 85.836, 164.397
Angle α, β, γ (deg.)82.929, 81.768, 71.281
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Antibody , 2 types, 16 molecules LACEIOQMHBDFJPRN

#1: Antibody
Fab h2E2 light chain


Mass: 22768.576 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody
Fab h2E2 heavy chain


Mass: 23720.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 193 molecules

#3: Chemical
ChemComp-BCG / 3-(BENZOYLOXY)-8-METHYL-8-AZABICYCLO[3.2.1]OCTANE-2-CARBOXYLIC ACID / BENZOYLECGONINE


Mass: 289.326 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C16H19NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: G10 of PEG/Ion HT (2% Tascimate pH 7.0, 0.1 M HEPES pH 7.5, 20% PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.63→50 Å / Num. obs: 104134 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 46.63 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.074 / Rrim(I) all: 0.14 / Χ2: 1.405 / Net I/σ(I): 13.9
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 5217 / CC1/2: 0.572 / Rpim(I) all: 0.537 / Rrim(I) all: 0.97 / Χ2: 0.881 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T2N

3t2n


Resolution: 2.63→38.67 Å / SU ML: 0.3452 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.689
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 5131 4.93 %random
Rwork0.1851 98920 --
obs0.1881 104051 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.54 Å2
Refinement stepCycle: LAST / Resolution: 2.63→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24869 0 220 173 25262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004125693
X-RAY DIFFRACTIONf_angle_d0.719935118
X-RAY DIFFRACTIONf_chiral_restr0.05014087
X-RAY DIFFRACTIONf_plane_restr0.00464464
X-RAY DIFFRACTIONf_dihedral_angle_d20.63189041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-2.660.34561040.28421995X-RAY DIFFRACTION58.94
2.66-2.690.37881740.27163405X-RAY DIFFRACTION98.7
2.69-2.720.33651480.26273298X-RAY DIFFRACTION98.71
2.72-2.760.33261430.25193334X-RAY DIFFRACTION98.75
2.76-2.790.32771790.25153405X-RAY DIFFRACTION99.01
2.79-2.830.32031810.24133289X-RAY DIFFRACTION98.92
2.83-2.870.35451550.24743393X-RAY DIFFRACTION99.05
2.87-2.910.29712000.24623292X-RAY DIFFRACTION98.9
2.91-2.960.36531770.25043362X-RAY DIFFRACTION98.94
2.96-3.010.35751610.24243303X-RAY DIFFRACTION98.94
3.01-3.060.28761720.2323406X-RAY DIFFRACTION99.03
3.06-3.120.27641480.2123301X-RAY DIFFRACTION98.94
3.12-3.170.26271770.20913428X-RAY DIFFRACTION98.96
3.17-3.240.28061890.20713274X-RAY DIFFRACTION98.91
3.24-3.310.29221790.20323365X-RAY DIFFRACTION98.88
3.31-3.390.26261740.20623332X-RAY DIFFRACTION98.9
3.39-3.470.26931560.18613347X-RAY DIFFRACTION98.84
3.47-3.570.24961810.18443330X-RAY DIFFRACTION98.99
3.57-3.670.26111760.183356X-RAY DIFFRACTION98.94
3.67-3.790.26211660.17783319X-RAY DIFFRACTION99.09
3.79-3.920.25061670.17593394X-RAY DIFFRACTION99
3.92-4.080.21011700.15583353X-RAY DIFFRACTION99.04
4.08-4.270.2091760.1483313X-RAY DIFFRACTION99.03
4.27-4.490.191840.13733331X-RAY DIFFRACTION99.15
4.49-4.770.18051780.13343362X-RAY DIFFRACTION99.19
4.77-5.140.20271590.14863352X-RAY DIFFRACTION99.18
5.14-5.660.21171780.15843355X-RAY DIFFRACTION99.47
5.66-6.470.2261780.18863358X-RAY DIFFRACTION99.27
6.47-8.140.21961880.18423320X-RAY DIFFRACTION99.26
8.14-38.670.19362130.16933248X-RAY DIFFRACTION97.03

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