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- PDB-1czw: STRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT -

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Basic information

Entry
Database: PDB / ID: 1czw
TitleSTRUCTURE OF THE W34A MUTANT OF SHIGA-LIKE TOXIN I B SUBUNIT
ComponentsSHIGA TOXIN B-CHAIN
KeywordsTOXIN / BACTERIAL TOXIN / SUGAR RECEPTOR BINDING DOMAIN / PROTEIN-CARBOHYDRATE RECOGNITION / OB-FOLD
Function / homology
Function and homology information


modulation of host virulence by virus / hemolysis by symbiont of host erythrocytes / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Shiga-like toxin 1 subunit B / Shiga-like toxin 1 subunit B
Similarity search - Component
Biological speciesPhage h30 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsLing, H. / Boodhoo, A. / Brunton, J.L. / Read, R.J.
CitationJournal: To be Published
Title: A native structure of the W34A mutant at 2.5 A
Authors: Ling, H. / Boodhoo, A. / Brunton, J.L. / Read, R.J.
History
DepositionSep 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA TOXIN B-CHAIN
B: SHIGA TOXIN B-CHAIN
C: SHIGA TOXIN B-CHAIN
D: SHIGA TOXIN B-CHAIN
E: SHIGA TOXIN B-CHAIN
F: SHIGA TOXIN B-CHAIN
G: SHIGA TOXIN B-CHAIN
H: SHIGA TOXIN B-CHAIN
I: SHIGA TOXIN B-CHAIN
J: SHIGA TOXIN B-CHAIN


Theoretical massNumber of molelcules
Total (without water)75,83510
Polymers75,83510
Non-polymers00
Water4,756264
1
A: SHIGA TOXIN B-CHAIN
B: SHIGA TOXIN B-CHAIN
C: SHIGA TOXIN B-CHAIN
D: SHIGA TOXIN B-CHAIN
E: SHIGA TOXIN B-CHAIN


Theoretical massNumber of molelcules
Total (without water)37,9185
Polymers37,9185
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-32 kcal/mol
Surface area13600 Å2
MethodPISA
2
F: SHIGA TOXIN B-CHAIN
G: SHIGA TOXIN B-CHAIN
H: SHIGA TOXIN B-CHAIN
I: SHIGA TOXIN B-CHAIN
J: SHIGA TOXIN B-CHAIN


Theoretical massNumber of molelcules
Total (without water)37,9185
Polymers37,9185
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-32 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.550, 108.920, 57.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
SHIGA TOXIN B-CHAIN


Mass: 7583.501 Da / Num. of mol.: 10 / Fragment: SHIGA-LIKE TOXIN I BINDING DOMAIN / Mutation: W34A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage h30 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P69178, UniProt: P69179*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 15% PEG 4000 0.2 M MGCL2 5% DIOXANE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 22, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→48.6 Å / Num. all: 24009 / Num. obs: 23240 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 38.53 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.5
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.365 / % possible all: 53.3

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
CNSrefinement
RefinementResolution: 2.5→48.6 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD F TARGET, WITH NCS RESTRAINTS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1243 5.2 %THIN SHELLS THROUGH WHOLE RESOLUTION RANGE
Rwork0.182 ---
obs0.182 23240 96.8 %-
all-24009 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.394 Å2--
2---1.004 Å2-
3---1.398 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 0 264 5574
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01291
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_deg1.9669
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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