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- PDB-1crz: CRYSTAL STRUCTURE OF THE E. COLI TOLB PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1crz
TitleCRYSTAL STRUCTURE OF THE E. COLI TOLB PROTEIN
ComponentsTOLB PROTEIN
KeywordsTOXIN BINDING PROTEIN / TWO DOMAINS: BETA PROPELLER AND ALPHA/BETA FOLD
Function / homology
Function and homology information


cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / protein domain specific binding ...cellular response to bacteriocin / regulation of membrane invagination / bacteriocin transport / protein import / cell division site / protein transport / outer membrane-bounded periplasmic space / periplasmic space / cell cycle / protein domain specific binding / cell division / protein-containing complex binding / protein-containing complex / membrane
Similarity search - Function
TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase ...TolB, N-terminal domain / TolB, N-terminal / Tol-Pal system protein TolB / TolB amino-terminal domain / WD40-like beta propeller / WD40-like Beta Propeller Repeat / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tol-Pal system protein TolB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsAbergel, C. / Bouveret, E. / Claverie, J.-M. / Brown, K. / Rigal, A. / Lazdunski, C. / Benedetti, H.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 A resolution.
Authors: Abergel, C. / Bouveret, E. / Claverie, J.M. / Brown, K. / Rigal, A. / Lazdunski, C. / Benedetti, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization and preliminary crystallographic study of a component of the E. coli Tol system: TolB
Authors: Abergel, C. / Rigal, A. / Chenivesse, S. / Lazdunski, C. / Claverie, J.-M. / Bouveret, E. / Benedetti, H.
History
DepositionAug 16, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_residues
Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOLB PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,2081
Polymers43,2081
Non-polymers00
Water8,251458
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.180, 40.500, 76.300
Angle α, β, γ (deg.)90.00, 110.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TOLB PROTEIN


Mass: 43207.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PTOLBHIS / Production host: Escherichia coli (E. coli) / References: UniProt: P0A855
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.11 Å3/Da / Density % sol: 41.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, SODIUM CHLORIDE, TRIS, TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Method: unknown
Details: Bourveret, E., (1998) These et Doctrat. Universite Aix-Marseille II.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11051
21
31
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM1410.9787
SYNCHROTRONESRF BM1420.9789
SYNCHROTRONESRF BM1430.8856
Detector
TypeIDDetectorDate
MARRESEARCH1CCDMay 11, 1999
2
3
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97891
30.88561
ReflectionResolution: 1.95→20 Å / Num. all: 25148 / Num. obs: 25138 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 17.751 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 7.9
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.228 / % possible all: 84.8
Reflection
*PLUS
Num. measured all: 360642
Reflection shell
*PLUS
% possible obs: 84.8 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.95→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2495 -RANDOM
Rwork0.238 ---
all0.188 25138 --
obs0.188 25138 94.5 %-
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 0 458 3488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.7
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
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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