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- PDB-4m3j: Structure of a single-domain camelid antibody fragment cAb-H7S sp... -

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Basic information

Entry
Database: PDB / ID: 4m3j
TitleStructure of a single-domain camelid antibody fragment cAb-H7S specific of the BlaP beta-lactamase from Bacillus licheniformis
ComponentsCamelid heavy-chain antibody variable fragment cAb-H7S
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Antigen binding / beta-lactamase binding antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 27, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Camelid heavy-chain antibody variable fragment cAb-H7S
B: Camelid heavy-chain antibody variable fragment cAb-H7S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2424
Polymers27,0502
Non-polymers1922
Water75742
1
A: Camelid heavy-chain antibody variable fragment cAb-H7S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6212
Polymers13,5251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Camelid heavy-chain antibody variable fragment cAb-H7S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6212
Polymers13,5251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-28 kcal/mol
Surface area11470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.562, 54.615, 83.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Camelid heavy-chain antibody variable fragment cAb-H7S


Mass: 13524.937 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)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 uL 0.2 M ammonium sulphate 0.1 M NaAc, pH 4.6, 25% PEG4000 + 0.2 uL cAb-H7S 15 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: 1.95→45.7 Å / Num. all: 18390 / Num. obs: 18390 / % possible obs: 99.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 16.2
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2514 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→45.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.72 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25213 941 5.1 %RANDOM
Rwork0.20595 ---
obs0.20812 17403 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.937 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0 Å2
2---0.16 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1742 0 10 42 1794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9482404
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7723.80371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85415288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.451512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021326
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: 1.95→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 71 -
Rwork0.269 1037 -
obs-1037 90.15 %
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)
11.9788-7.9002-0.052532.2551.41226.9969-0.07080.1649-0.50020.4448-0.49251.81520.2285-0.57410.56330.0557-0.0435-0.01120.252-0.14430.3932-8.639-14.48319.153
20.4461-0.87890.11932.3915-0.29651.26720.0380.1334-0.00870.0946-0.0767-0.0118-0.0255-0.09310.03870.1610.01060.00640.18020.00050.2042-2.167-4.84514.956
31.3043-1.6946-0.20595.44140.92621.24080.06560.3104-0.05960.0468-0.02940.09090.0057-0.0975-0.03620.12950.0119-0.01630.20850.00970.172-6.597-5.51410.655
42.8213-3.2718-0.36898.28181.51871.69080.08130.4473-0.22750.3346-0.32960.57810.276-0.27880.24830.11770.0063-0.00340.2847-0.02070.179-9.337-10.60411.573
53.07450.07496.3281.14910.623915.80490.02610.16740.0219-0.16680.1502-0.2829-0.19720.6479-0.17630.1036-0.090.08310.1655-0.04740.197323.0088.3595.775
62.58160.887-1.09731.30330.31531.8798-0.00490.1125-0.2176-0.11650.1503-0.1297-0.20720.0575-0.14540.1606-0.00470.06130.1788-0.03810.187614.62.1923.309
72.43871.08921.91821.72372.52134.90220.06760.0196-0.2471-0.27370.1125-0.1977-0.35950.1951-0.18010.11640.02010.05810.1722-0.04070.194618.067-0.9933.287
81.36251.91743.66624.86067.177713.4622-0.151-0.0801-0.0675-0.43520.009-0.2415-0.44620.29750.1420.1123-0.0330.09080.2983-0.03270.261425.111.5333.351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 82
3X-RAY DIFFRACTION3A83 - 102
4X-RAY DIFFRACTION4A103 - 120
5X-RAY DIFFRACTION5B1 - 19
6X-RAY DIFFRACTION6B20 - 80
7X-RAY DIFFRACTION7B81 - 106
8X-RAY DIFFRACTION8B107 - 119

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