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- PDB-4m3k: Structure of a single domain camelid antibody fragment cAb-H7S in... -

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Basic information

Entry
Database: PDB / ID: 4m3k
TitleStructure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis
Components
  • Beta-lactamase
  • Camelid heavy-chain antibody variable fragment cAb-H7S
KeywordsHYDROLASE/IMMUNE SYSTEM / immunoglobulin fold / antigen binding / beta-lactamase-antibody complex / 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: 1.48 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
DepositionAug 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-H7S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0084
Polymers43,9372
Non-polymers712
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-27 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.818, 42.940, 74.818
Angle α, β, γ (deg.)90.00, 105.29, 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.: 1 / Fragment: UNP residues 44-307
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-H7S


Mass: 13524.937 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMES4 / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
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: 1.83 Å3/Da / Density % sol: 32.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 uL 0.2 M (NH4)Cl 20 % PEG3350 + 0.2 uL complex 14.2 mg/ml 20 mM tris, 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: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.48→42.94 Å / Num. all: 52300 / Num. obs: 52300 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7316 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→36.9 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.315 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1947 2662 5.1 %RANDOM
Rwork0.16121 ---
obs0.16292 49631 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.19 Å2
2---0.09 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.48→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 2 269 3161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023005
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9674071
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1765386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2324.478134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07515536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4081523
X-RAY DIFFRACTIONr_chiral_restr0.1120.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212239
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_restr2.76433005
X-RAY DIFFRACTIONr_sphericity_free23.595573
X-RAY DIFFRACTIONr_sphericity_bonded8.39753151
LS refinement shellResolution: 1.48→1.521 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 183 -
Rwork0.353 3259 -
obs-3259 91.15 %
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)
10.6572-0.9057-0.05592.40640.04750.1980.07170.05390.04090.0157-0.0668-0.1257-0.10670.1135-0.00490.0952-0.0317-0.06890.163-0.00590.21813.11811.89-17.284
20.23780.12540.07280.28610.15420.32190.00310.0387-0.00110.0028-0.00820.01520.00120.00230.00510.02560.0087-0.06610.14630.00060.1773-19.152-6.769-24.186
32.6887-0.2070.99431.1808-0.3140.60930.0538-0.07740.01430.1129-0.1018-0.03810.0362-0.00920.0480.0484-0.0058-0.05180.14330.00670.1663-12.257-6.481-10.545
40.4552-0.4664-0.2171.26820.32760.5123-0.0173-0.0482-0.0280.093-0.0075-0.01770.0369-0.00030.02480.0346-0.0046-0.06770.13450.00210.1695-8.7170.87-13.46
50.6583-0.92390.49093.5102-1.36140.5717-0.00580.0534-0.0189-0.0835-0.0432-0.14540.02010.03620.04890.03150.0083-0.05540.14080.00020.1823-4.337-9.93-28.379
60.686-0.3766-0.25480.80680.04750.5987-0.02140.06270.04520.0056-0.0077-0.02460.00940.05120.02910.02330.0059-0.06390.15090.00020.1813-3.1015.692-26.086
73.2455-0.2957-0.90110.4780.01311.14920.02320.03480.03270.0016-0.0274-0.0028-0.18240.07830.00430.0541-0.0101-0.06340.12180.00230.1978-3.97414.717-22.279
814.9251-8.5062-17.012514.37968.331619.8953-0.70010.8457-0.659-0.4619-0.33430.9140.9387-1.08531.03440.119-0.0817-0.0290.2711-0.09910.4516-40.381-15.924-14.189
91.1083-1.196-0.98132.59562.06582.4196-0.1186-0.2035-0.02970.00890.07410.07540.05410.02280.04460.04690.0005-0.04510.1592-0.00530.1898-42.139-7.132-1.742
101.1091-1.2435-1.08621.74091.67641.7254-0.00960.031-0.02220.124-0.11840.05740.1733-0.09030.1280.0976-0.0108-0.05340.16640.00010.2094-30.781-15.075-13.849
112.3094-1.41042.43083.0823-4.46398.4269-0.0926-0.16670.11240.19350.0804-0.0046-0.4231-0.03040.01230.04120.0032-0.05750.1328-0.01910.1958-31.71-1.082-11.782
121.5512-1.0623-1.18681.07050.81321.2091-0.1544-0.24980.01140.1340.1032-0.02660.17870.14020.05120.0559-0.0005-0.05640.2052-0.00910.1822-30.271-10.357-3.279
130.6059-0.4903-0.82210.56350.63191.4486-0.0231-0.0139-0.0067-0.01140.02950.02770.0225-0.0447-0.00640.0262-0.0026-0.06050.1449-0.01440.1791-34.385-9.021-13.509
142.8555-2.7657-3.00563.32622.81213.7733-0.02620.2299-0.0759-0.0075-0.10830.08970.0755-0.31090.13450.0256-0.0119-0.05820.1681-0.02320.1977-37.562-9.479-15.41
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 61
2X-RAY DIFFRACTION2A62 - 145
3X-RAY DIFFRACTION3A146 - 167
4X-RAY DIFFRACTION4A168 - 195
5X-RAY DIFFRACTION5A196 - 217
6X-RAY DIFFRACTION6A218 - 269
7X-RAY DIFFRACTION7A270 - 291
8X-RAY DIFFRACTION8B2 - 8
9X-RAY DIFFRACTION9B9 - 24
10X-RAY DIFFRACTION10B25 - 38
11X-RAY DIFFRACTION11B39 - 50
12X-RAY DIFFRACTION12B51 - 86
13X-RAY DIFFRACTION13B87 - 103
14X-RAY DIFFRACTION14B104 - 120

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