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- PDB-1e2a: ENZYME IIA FROM THE LACTOSE SPECIFIC PTS FROM LACTOCOCCUS LACTIS -

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Basic information

Entry
Database: PDB / ID: 1e2a
TitleENZYME IIA FROM THE LACTOSE SPECIFIC PTS FROM LACTOCOCCUS LACTIS
ComponentsENZYME IIA
KeywordsTRANSFERASE / ENZYME IIA / HELICAL BUNDLES / PTS / PHOSPHOTRANSFERASE SYSTEM
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PTS system lactose-specific EIIA component
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT, ANOMALOUS SCATTERING (SIRAS) / Resolution: 2.3 Å
AuthorsSliz, P. / Engelmann, R. / Hengstenberg, W. / Pai, E.F.
Citation
Journal: Structure / Year: 1997
Title: The structure of enzyme IIAlactose from Lactococcus lactis reveals a new fold and points to possible interactions of a multicomponent system.
Authors: Sliz, P. / Engelmann, R. / Hengstenberg, W. / Pai, E.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization and Preliminary Structural Studies of Lactose-Specific Enzyme Iia from Lactococcus Lactis
Authors: Sliz, P. / Schorter, K.H. / De Vos, W.M. / Pai, E.F.
History
DepositionApr 25, 1997Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENZYME IIA
B: ENZYME IIA
C: ENZYME IIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4144
Polymers34,3893
Non-polymers241
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-55 kcal/mol
Surface area12140 Å2
MethodPISA
2
A: ENZYME IIA
B: ENZYME IIA
C: ENZYME IIA
hetero molecules

A: ENZYME IIA
B: ENZYME IIA
C: ENZYME IIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8278
Polymers68,7796
Non-polymers492
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14020 Å2
ΔGint-103 kcal/mol
Surface area23160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.900, 90.900, 82.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0704, -0.0668, 0.9953), (0.9846, -0.1557, -0.0801), (0.1603, 0.9855, 0.0548)32.8913, -21.3201, -16.5359
2given(0.0725, 0.9851, 0.1561), (-0.065, -0.1515, 0.9863), (0.9952, -0.0817, 0.0531)21.1148, 14.8587, -33.3513
3given(0.0946, -0.0947, 0.991), (0.9872, -0.1193, -0.1057), (0.1282, 0.9883, 0.0822)32.3799, -21.9091, -15.1405

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Components

#1: Protein ENZYME IIA / ENZYME III / LACTOSE-SPECIFIC IIA COMPONENT


Mass: 11463.118 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: MG1820 / Gene: LACF / Production host: Escherichia coli (E. coli)
References: UniProt: P23532, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.4
Details: CRYSTALS WERE OBTAINED BY THE SITTING-DROP VAPOR-DIFFUSION TECHNIQUE AT ROOM TEMPERATURE USING A SMALL INCREASE IN THE PHOSPHATE BUFFER. THE PROTEIN SOLUTION WAS MIXED WITH 0.15M NA/K ...Details: CRYSTALS WERE OBTAINED BY THE SITTING-DROP VAPOR-DIFFUSION TECHNIQUE AT ROOM TEMPERATURE USING A SMALL INCREASE IN THE PHOSPHATE BUFFER. THE PROTEIN SOLUTION WAS MIXED WITH 0.15M NA/K PHOSPHATE BUFFER, PH 6.4. THE LARGEST CRYSTALS APPEARED IN CIRCA A WEEK., vapor diffusion - sitting drop
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 25 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2150 mMsodium potassium phosphate1drop
3400 mMsodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. obs: 16632 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rsym value: 0.086 / Net I/σ(I): 18.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.36 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.363

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT, ANOMALOUS SCATTERING (SIRAS)
Resolution: 2.3→8 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.24 -10 %RANDOM
Rwork0.19 ---
obs0.19 15009 97.7 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 1 56 2421
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg0.93
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.94
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.037
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.037

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