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- PDB-8cge: The crystal structure of a cobalt-bound scFv reveals a Tetrameric... -

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Basic information

Entry
Database: PDB / ID: 8cge
TitleThe crystal structure of a cobalt-bound scFv reveals a Tetrameric polyHistidine motif (TetrHis)
ComponentsSingle Chain Fv 2A2
KeywordsMETAL BINDING PROTEIN / Single Chain Fragment Variable Antibody / tetrameric polyhistidine TetrHis motif / cobalt-bound
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHealey, R.D. / Hoh, F. / Granier, S. / Leyrat, C.
Funding support France, 1items
OrganizationGrant numberCountry
Not funded France
CitationJournal: Commun Chem / Year: 2023
Title: Structure, dynamics and transferability of the metal-dependent polyhistidine tetramerization motif TetrHis for single-chain Fv antibodies.
Authors: Healey, R.D. / Couillaud, L. / Hoh, F. / Mouhand, A. / Fouillen, A. / Couvineau, P. / Granier, S. / Leyrat, C.
History
DepositionFeb 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single Chain Fv 2A2
B: Single Chain Fv 2A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,52222
Polymers64,6242
Non-polymers1,89820
Water3,531196
1
A: Single Chain Fv 2A2
B: Single Chain Fv 2A2
hetero molecules

A: Single Chain Fv 2A2
B: Single Chain Fv 2A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,04444
Polymers129,2484
Non-polymers3,79640
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15760 Å2
ΔGint-457 kcal/mol
Surface area39510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.496, 81.817, 111.045
Angle α, β, γ (deg.)90.000, 111.140, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 19 through 137 or resid 158 through 281))
d_2ens_1(chain "B" and resid 19 through 281)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNSERA1 - 119
d_12ens_1SERGLNA122 - 245
d_21ens_1GLNGLNB1 - 243

NCS oper: (Code: givenMatrix: (-0.586115834054, 0.369218282168, 0.721211542603), (0.169450102625, -0.81459115152, 0.554732294522), (0.792309845825, 0.447346751389, 0.414880696381)Vector: -3. ...NCS oper: (Code: given
Matrix: (-0.586115834054, 0.369218282168, 0.721211542603), (0.169450102625, -0.81459115152, 0.554732294522), (0.792309845825, 0.447346751389, 0.414880696381)
Vector: -3.44708737713, -17.3966670401, 9.17948883705)

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Components

#1: Antibody Single Chain Fv 2A2


Mass: 32311.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly)
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.2 Å3/Da / Density % sol: 61.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.01M cobalt chloride, 0.1M MES, pH6.5, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.999 / Wavelength: 0.999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.5→45.47 Å / Num. obs: 28177 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 44.77 Å2 / CC1/2: 0.989 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.6 Å / Num. unique obs: 635 / CC1/2: 0.491

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.17 Å / SU ML: 0.3325 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7089
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 1387 4.93 %
Rwork0.1902 26772 -
obs0.193 28159 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3847 0 93 196 4136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084030
X-RAY DIFFRACTIONf_angle_d1.31795477
X-RAY DIFFRACTIONf_chiral_restr0.0611572
X-RAY DIFFRACTIONf_plane_restr0.0076680
X-RAY DIFFRACTIONf_dihedral_angle_d6.3504535
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 6.03782312577 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.590.31551240.27952596X-RAY DIFFRACTION96.11
2.59-2.690.36551430.26942657X-RAY DIFFRACTION99.79
2.69-2.810.33571530.26122662X-RAY DIFFRACTION99.47
2.81-2.960.30881270.23612712X-RAY DIFFRACTION99.72
2.96-3.150.29931440.22682659X-RAY DIFFRACTION99.36
3.15-3.390.26091340.20772673X-RAY DIFFRACTION99.05
3.39-3.730.26361380.16932662X-RAY DIFFRACTION98.7
3.73-4.270.20711480.15862697X-RAY DIFFRACTION99.65
4.27-5.380.19791330.1432712X-RAY DIFFRACTION99.79
5.38-45.170.211430.18652742X-RAY DIFFRACTION98.87
Refinement TLS params.Method: refined / Origin x: -11.6715415952 Å / Origin y: -15.1313179124 Å / Origin z: -11.1290017382 Å
111213212223313233
T0.311960552534 Å2-0.0150743952843 Å2-0.0103249823062 Å2-0.276849074742 Å20.00687880269251 Å2--0.255773701025 Å2
L1.73043885784 °2-1.34736502209 °2-0.436403369665 °2-1.22144309885 °20.390553409583 °2--0.371490630005 °2
S-0.000976626001215 Å °-0.089819004487 Å °0.030099967413 Å °0.0152740759149 Å °0.0639119781358 Å °-0.0401037502366 Å °0.01411928023 Å °0.0552131559762 Å °-0.0641473601889 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-ID
1X-RAY DIFFRACTION1{ A|* }A
2X-RAY DIFFRACTION1{ B|* }B

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