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- PDB-1f3z: IIAGLC-ZN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1f3z
TitleIIAGLC-ZN COMPLEX
ComponentsGLUCOSE-SPECIFIC PHOSPHOCARRIER
KeywordsPHOSPHOTRANSFERASE / SIGNAL TRANSDUCTION / SUGAR TRANSPORT
Function / homology
Function and homology information


negative regulation of carbohydrate metabolic process / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / kinase activity / phosphorylation / membrane / metal ion binding / cytosol
Similarity search - Function
PTS EIIA domains phosphorylation site signature 1. / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Glucose Permease (Domain IIA) / Glucose Permease (Domain IIA) / Duplicated hybrid motif / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
PTS system glucose-specific EIIA component
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsFeese, M. / Comolli, L. / Meadow, N. / Roseman, S. / Remington, S.J.
CitationJournal: Biochemistry / Year: 1997
Title: Structural studies of the Escherichia coli signal transducing protein IIAGlc: implications for target recognition.
Authors: Feese, M.D. / Comolli, L. / Meadow, N.D. / Roseman, S. / Remington, S.J.
History
DepositionOct 9, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _pdbx_database_status.process_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4032
Polymers17,3381
Non-polymers651
Water41423
1
A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules

A: GLUCOSE-SPECIFIC PHOSPHOCARRIER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8074
Polymers34,6762
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Unit cell
Length a, b, c (Å)47.700, 47.700, 144.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GLUCOSE-SPECIFIC PHOSPHOCARRIER / EIIA-GLC


Mass: 17337.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: IIAGLC FAST-MISSING SEVEN N-TERMINAL AMINO ACIDS / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P69783, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.28 Å3/Da / Density % sol: 48.12 %
Crystal growpH: 8.5
Details: 0.1-0.3 M SODIUM ACETATE, 1MM ZINC ACETATE, 0.1 M TRIS BUFFER PH 8.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122-26 %PEG400011
20.1-0.3 Msodium acetate11
31 mMzinc acetate11
40.1 MTris-HCl11
56 mg/mlprotain12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 7578 / % possible obs: 61 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. measured all: 22910

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Processing

Software
NameVersionClassification
UNPUBLISHEDmodel building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
UNPUBLISHEDphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3G

1f3g


Resolution: 1.98→20 Å / Isotropic thermal model: TNT BCORREL V2.1 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.193 --
all-7578 -
obs-7578 61 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 300 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 1.98→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 1 23 1131
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01111221.5
X-RAY DIFFRACTIONt_angle_deg1.9815183
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009282
X-RAY DIFFRACTIONt_gen_planes0.0151616
X-RAY DIFFRACTIONt_it5.711221.5
X-RAY DIFFRACTIONt_nbd0.0222510
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.193
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0092
X-RAY DIFFRACTIONt_plane_restr0.0156

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