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- PDB-2nrj: Crystal Structure of Hemolysin binding component from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 2nrj
TitleCrystal Structure of Hemolysin binding component from Bacillus cereus
ComponentsHbl B protein
KeywordsTOXIN / Enterotoxin / Hemolysis / Transmembrane / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


hemolysis in another organism / : / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Hemolysin BL-binding component / Hbl B protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsMadegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2008
Title: X-ray crystal structure of the B component of Hemolysin BL from Bacillus cereus
Authors: Madegowda, M. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hbl B protein


Theoretical massNumber of molelcules
Total (without water)38,9351
Polymers38,9351
Non-polymers00
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.833, 28.549, 89.738
Angle α, β, γ (deg.)90.00, 105.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

21A-391-

HOH

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Components

#1: Protein Hbl B protein / Hemolysin A / Hemolysin BL HBL / binding component B / haemolytic enterotoxin


Mass: 38934.703 Da / Num. of mol.: 1 / Fragment: residues 32-375
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: hblA / Plasmid: pSGX4 (BS) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)+Codon+RIL / References: UniProt: Q9REG6, UniProt: P80172*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 4000, 0.2M Magnesium Chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9772 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 2.03→26.05 Å / Num. all: 20797 / Num. obs: 20797 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.5
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.272 / Num. unique all: 1974 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→26.05 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 92972.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The authors state that the missing residues listed in remark 465 are due to lack of electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.257 990 4.9 %RANDOM
Rwork0.213 ---
obs0.213 20360 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.8406 Å2 / ksol: 0.368405 e/Å3
Displacement parametersBiso mean: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20.31 Å2
2--4.71 Å20 Å2
3----6.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.03→26.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 0 199 2852
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.382
X-RAY DIFFRACTIONc_scangle_it3.552.5
LS refinement shellResolution: 2.03→2.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 144 4.5 %
Rwork0.25 3052 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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