[English] 日本語
Yorodumi
- PDB-3ab0: Crystal structure of complex of the Bacillus anthracis major spor... -

+
Open data


ID or keywords:

Loading...

-
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 proteinBritish Columbia Lacrosse Association
  • 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 / immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / immune response / extracellular space
Similarity search - Function
BclA, C-terminal domain / BclA C-terminal domain / 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 ...BclA, C-terminal domain / BclA C-terminal domain / 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 / Jelly Rolls / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein BclA protein / British Columbia Lacrosse Association / 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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more