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- PDB-3ab0: Crystal structure of complex of the Bacillus anthracis major spor... -

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Basic information

Entry
Database: PDB / ID: 3ab0
TitleCrystal structure of complex of the Bacillus anthracis major spore surface protein BclA with ScFv antibody fragment
Components
  • BclA protein
  • antibody ScFv fragment, heavy chain
  • antibody ScFv fragment, light chain
KeywordsIMMUNE SYSTEM / exosporium / anthrax / TBCLA / scFv complex
Function / homology
Function and homology information


immunoglobulin production / extracellular matrix structural constituent conferring tensile strength / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / extracellular matrix organization / extracellular matrix / immune response / extracellular space / extracellular region
Similarity search - Function
BclA, C-terminal domain / BclA C-terminal domain / Leader peptide, exosporium / : / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type ...BclA, C-terminal domain / BclA C-terminal domain / Leader peptide, exosporium / : / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / : / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Jelly Rolls / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa chain variable 4-54 / Ig heavy chain V region 914 / BclA protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsStreltsov, V.A.
CitationJournal: Proteins / Year: 2011
Title: Isolation, kinetic analysis, and structural characterization of an antibody targeting the Bacillus anthracis major spore surface protein BclA.
Authors: Nuttall, S.D. / Wilkins, M.L. / Streltsov, V.A. / Pontes-Braz, L. / Dolezal, O. / Tran, H. / Liu, C.Q.
History
DepositionNov 28, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 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: BclA protein
B: antibody ScFv fragment, heavy chain
C: antibody ScFv fragment, light chain
D: BclA protein
E: antibody ScFv fragment, heavy chain
F: antibody ScFv fragment, light chain


Theoretical massNumber of molelcules
Total (without water)75,4636
Polymers75,4636
Non-polymers00
Water25214
1
A: BclA protein
B: antibody ScFv fragment, heavy chain
C: antibody ScFv fragment, light chain


Theoretical massNumber of molelcules
Total (without water)37,7313
Polymers37,7313
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: BclA protein
E: antibody ScFv fragment, heavy chain
F: antibody ScFv fragment, light chain


Theoretical massNumber of molelcules
Total (without water)37,7313
Polymers37,7313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9170 Å2
ΔGint-39 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.448, 125.448, 125.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein BclA protein / major spore surface protein BclA


Mass: 13516.480 Da / Num. of mol.: 2 / Fragment: UNP residues 311-445
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: 34F2 (NMRC) / Gene: bclA / Plasmid: PFB45 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER(DE3)PLACI / References: UniProt: Q83WB0
#2: Antibody antibody ScFv fragment, heavy chain / A4D11 antibody scFv fragment


Mass: 12806.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A4D11 / Gene: 35G-5 / Plasmid: pGC / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P18527*PLUS
#3: Antibody antibody ScFv fragment, light chain / A4D11 antibody scFv fragment


Mass: 11408.620 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A4D11 / Gene: 35G-5 / Plasmid: pGC / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: J3QMZ0*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLEU 215 IS FIRST RESIDUE OF LINKER TO THE 6 HIS TAGS

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 3350, 0.2M potassium acetate, 25% PEG 3350, 0.2M magnesium chloride, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→44.35 Å / Num. obs: 11525 / % possible obs: 98.2 % / Observed criterion σ(I): 1 / Redundancy: 18.1 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 18.8
Reflection shellResolution: 3.09→3.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1 / % possible all: 80

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0101refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z5W, 1QOK

2z5w

1qok


Resolution: 3.09→44.35 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 36.883 / SU ML: 0.285 / Isotropic thermal model: ISOTROPIC & TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26471 558 4.6 %RANDOM
Rwork0.19707 ---
obs0.20029 11525 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.946 Å2
Refinement stepCycle: LAST / Resolution: 3.09→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 0 14 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225414
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.971.967370
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48923.667180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75215846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7621522
X-RAY DIFFRACTIONr_chiral_restr0.0570.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214000
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_it0.1421.53538
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.26325700
X-RAY DIFFRACTIONr_scbond_it0.26731876
X-RAY DIFFRACTIONr_scangle_it0.4664.51670
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.093→3.173 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 41 -
Rwork0.305 678 -
obs--79.8 %
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)
11.8579-0.34490.04081.1933-0.31041.49980.06960.00910.1643-0.0315-0.05760.1102-0.0539-0.0945-0.0120.1322-0.02650.060.1331-0.02740.1527-30.931-26.25643.771
20.5334-0.5035-0.91143.81110.16673.2709-0.0209-0.31890.07950.3342-0.00240.09840.01630.28470.02330.1218-0.0310.12260.2848-0.10880.1744-35.837-21.30671.272
31.3816-1.60150.05122.89150.40392.38490.0958-0.10170.32030.10990.15650.0449-0.5515-0.0536-0.25230.3196-0.06210.24760.11140.00240.3356-31.612-3.2459.782
41.74380.69770.27932.1088-0.69122.0146-0.08330.06460.09440.08910.0440.1976-0.1917-0.06420.03930.1273-0.042-0.02750.10980.0330.12-5.099-0.41550.32
53.052-0.18490.6741.8399-0.04783.896-0.050.1859-0.0355-0.4742-0.01840.14430.1509-0.06890.06850.1436-0.0152-0.05170.08520.09450.1599-10.0724.44822.794
63.9584-0.34250.23640.0858-0.22581.50910.13870.31060.4877-0.0285-0.0030.0491-0.0281-0.2383-0.13570.1062-0.0946-0.09670.23660.13870.2999-28.0620.17134.307
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 215
2X-RAY DIFFRACTION2B1 - 117
3X-RAY DIFFRACTION3C1 - 106
4X-RAY DIFFRACTION4D80 - 215
5X-RAY DIFFRACTION5E1 - 117
6X-RAY DIFFRACTION6F1 - 106

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