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- PDB-7tjc: VHH Chl-B2 in complex with Chloramphenicol -

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Basic information

Entry
Database: PDB / ID: 7tjc
TitleVHH Chl-B2 in complex with Chloramphenicol
ComponentsVHH-Chl-B2
KeywordsIMMUNE SYSTEM / Antibiotic-binding protein / nanobody / VHH
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CHLORAMPHENICOL
Function and homology information
Biological speciesVicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsNordeen, S.A. / Schwartz, T.U.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM77537 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM007287 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Structure and specificity of an anti-chloramphenicol single domain antibody for detection of amphenicol residues.
Authors: Swofford, C.A. / Nordeen, S.A. / Chen, L. / Desai, M.M. / Chen, J. / Springs, S.L. / Schwartz, T.U. / Sinskey, A.J.
History
DepositionJan 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 23, 2024Group: Structure summary / Category: 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: VHH-Chl-B2
B: VHH-Chl-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8095
Polymers30,0712
Non-polymers7383
Water4,684260
1
A: VHH-Chl-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4513
Polymers15,0361
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: VHH-Chl-B2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3592
Polymers15,0361
Non-polymers3231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.219, 66.553, 93.165
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody VHH-Chl-B2


Mass: 15035.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR-
#2: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.16 Å3/Da / Density % sol: 43 % / Description: rod-shaped
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM sodium acetate, 1 M di-ammonium hydrogen phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.35→54.15 Å / Num. obs: 59730 / % possible obs: 99.7 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 2.4 / Net I/σ(I): 9.1
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 6000 / CC1/2: 0.739 / Rpim(I) all: 0.398 / % possible all: 98.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.20rc3_4406refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZQ

1bzq


Resolution: 1.35→54.15 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1997 3.34 %
Rwork0.2004 57733 -
obs0.2015 59730 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.73 Å2 / Biso mean: 21.71 Å2 / Biso min: 9.92 Å2
Refinement stepCycle: final / Resolution: 1.35→54.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 46 261 2195
Biso mean--25.83 34.57 -
Num. residues----246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.380.3561360.31053890402695
1.38-1.420.29131390.257640724211100
1.42-1.460.27581420.220140804222100
1.46-1.510.27881410.200240964237100
1.51-1.560.22451410.199240784219100
1.56-1.630.24231420.199641024244100
1.63-1.70.25561420.193141054247100
1.7-1.790.2371430.190541184261100
1.79-1.90.26731430.192741214264100
1.9-2.050.23011420.186141404282100
2.05-2.250.25521440.185441394283100
2.25-2.580.2591450.202441774322100
2.58-3.250.23071450.206842144359100
3.25-54.150.19771520.196444014553100

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