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- PDB-1iib: CRYSTAL STRUCTURE OF IIBCELLOBIOSE FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1iib
TitleCRYSTAL STRUCTURE OF IIBCELLOBIOSE FROM ESCHERICHIA COLI
ComponentsENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM
KeywordsPHOSPHOTRANSFERASE / PHOSPHOENOLPYRUVATE DEPENDENT PHOSPHOTRANSFERASE SYSTEM / IIB ENZYMES / CYSTEINE PHOSPHORYLATION
Function / homology
Function and homology information


protein-Npi-phosphohistidine-N,N'-diacetylchitobiose phosphotransferase / protein-phosphocysteine-N,N'-diacetylchitobiose phosphotransferase system transporter activity / N,N'-diacetylchitobiose import / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / cytosol
Similarity search - Function
: / Phosphotransferase system, EIIB component, type 3 / PTS_EIIB type-3 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system N,N'-diacetylchitobiose-specific EIIB component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsVan Montfort, R.L.M. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier, M.H. / Thunnissen, M.M.G.M. / Robillard, G.T. / Dijkstra, B.W.
CitationJournal: Structure / Year: 1997
Title: The structure of an energy-coupling protein from bacteria, IIBcellobiose, reveals similarity to eukaryotic protein tyrosine phosphatases.
Authors: van Montfort, R.L. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier Jr., M.H. / Thunnissen, M.M. / Robillard, G.T. / Dijkstra, B.W.
History
DepositionDec 23, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Other
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM
B: ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM


Theoretical massNumber of molelcules
Total (without water)22,8472
Polymers22,8472
Non-polymers00
Water2,306128
1
A: ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM


Theoretical massNumber of molelcules
Total (without water)11,4231
Polymers11,4231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM


Theoretical massNumber of molelcules
Total (without water)11,4231
Polymers11,4231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.791, 31.782, 60.253
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.995894, -0.002445, -0.090488), (-0.002788, -0.999989, -0.003668), (-0.090478, 0.003906, -0.995891)
Vector: -30.023, 50.236, 92.781)

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Components

#1: Protein ENZYME IIB OF THE CELLOBIOSE-SPECIFIC PHOSPHOTRANSFERASE SYSTEM


Mass: 11423.449 Da / Num. of mol.: 2 / Fragment: ENZYME IIB / Mutation: C10S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cellular location: CYTOPLASM / Gene: CELA / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: P69795, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.2 Å3/Da / Density % sol: 44 %
Description: THE NATIVE DATASET USED WAS OBTAINED BY MERGING OF A 2.6 ANGSTROM IN HOUSE DATA SET WITH A 1.8 ANGSTROM X31 DATASET. THE STATISTICS OF THE X-31 DATASET ARE GIVEN ABOVE.
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.25 mg/mlprotein1drop
216-16.5 %(w/v)PEG40001drop
30.05 MBES/NaOH1drop
40.5 mM1dropNaN3
55 %(v/v)2-propanol1drop
60.5 %(w/v)benzamidine/HCl1drop
718-19 %PEG40001reservoir
85 %(v/v)2-propanol1reservoir
90.1 MBES/NaOH1reservoir
101 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 16165 / % possible obs: 82.8 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.061
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.122 / % possible all: 74.1
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Rmerge(I) obs: 0.122

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
BIOMOLdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→10 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Details: NCS-RESTRAINTS RELEASED AT 1.8 ANGSTROM RESOLUTION
RfactorNum. reflection% reflectionSelection details
Rfree0.241 -10 %RANDOM
Rwork0.187 ---
obs0.187 16419 87.3 %-
Displacement parametersBiso mean: 21.9 Å2
Refine analyzeLuzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 0 128 1678
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_1996.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37

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