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- PDB-4n1h: Structure of a single-domain camelid antibody fragment cAb-F11N i... -

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Basic information

Entry
Database: PDB / ID: 4n1h
TitleStructure of a single-domain camelid antibody fragment cAb-F11N in complex with the BlaP beta-lactamase from Bacillus licheniformis
Components
  • Beta-lactamase
  • Camelid heavy-chain antibody variable fragment cAb-F11N
KeywordsHYDROLASE/IMMUNE SYSTEM / Immunoglobulin fold / Antigen binding / HYDROLASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. ...Beta-lactamase / Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus licheniformis (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPain, C. / Kerff, F. / Herman, R. / Sauvage, E. / Preumont, S. / Charlier, P. / Dumoulin, M.
CitationJournal: To be Published
Title: Probing the mechanism of aggregation of polyQ model proteins with camelid heavy-chain antibody fragments
Authors: Pain, C. / Cosolo, A. / Preumont, S. / Scarafone, N. / Thorn, D. / Herman, R. / Spiegel, H. / Pardon, E. / Matagne, A. / Charlier, P. / Steyaert, J. / Damblon, C. / Kerff, F. / Esposito, G. / Dumoulin, M.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
B: Camelid heavy-chain antibody variable fragment cAb-F11N
C: Beta-lactamase
D: Camelid heavy-chain antibody variable fragment cAb-F11N


Theoretical massNumber of molelcules
Total (without water)90,0434
Polymers90,0434
Non-polymers00
Water32418
1
A: Beta-lactamase
B: Camelid heavy-chain antibody variable fragment cAb-F11N


Theoretical massNumber of molelcules
Total (without water)45,0212
Polymers45,0212
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-lactamase
D: Camelid heavy-chain antibody variable fragment cAb-F11N


Theoretical massNumber of molelcules
Total (without water)45,0212
Polymers45,0212
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.088, 89.821, 75.749
Angle α, β, γ (deg.)90.00, 95.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase / Penicillinase / Large exopenicillinase / Small exopenicillinase


Mass: 30412.311 Da / Num. of mol.: 2 / Fragment: UNP residues 44-307 / Mutation: ProGly insertion between residues 197 and 198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (bacteria) / Gene: penP, blaP / Plasmid: pNY / Production host: Escherichia coli (E. coli) / References: UniProt: P00808, beta-lactamase
#2: Antibody Camelid heavy-chain antibody variable fragment cAb-F11N


Mass: 14609.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 uL acetate 0.1 M, pH 4.6, 12 % P4K + 0.1 uL protein complex at 14 mg/mL in Tris 20 mM, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 3→75.44 Å / Num. all: 15849 / Num. obs: 15849 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.185 / Net I/σ(I): 5.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M3J

4m3j


Resolution: 3→75.44 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R Free: 0.548 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28449 794 5 %RANDOM
Rwork0.20844 ---
obs0.2122 15041 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.72 Å2
2---5.09 Å20 Å2
3---5.39 Å2
Refinement stepCycle: LAST / Resolution: 3→75.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5944 0 0 18 5962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.026045
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9628179
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.13524.513277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.589151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0661544
X-RAY DIFFRACTIONr_chiral_restr0.0830.2919
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 65 -
Rwork0.282 1084 -
obs--99.65 %

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