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- PDB-2gpr: GLUCOSE PERMEASE IIA FROM MYCOPLASMA CAPRICOLUM -

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Basic information

Entry
Database: PDB / ID: 2gpr
TitleGLUCOSE PERMEASE IIA FROM MYCOPLASMA CAPRICOLUM
ComponentsGLUCOSE-PERMEASE IIA COMPONENT
KeywordsPHOSPHOTRANSFERASE / GLUCOSE PERMEASE / ENZYME IIA / MYCOPLASMA
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / cytoplasm
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 speciesMycoplasma capricolum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHuang, K. / Herzberg, O.
CitationJournal: Structure / Year: 1998
Title: A promiscuous binding surface: crystal structure of the IIA domain of the glucose-specific permease from Mycoplasma capricolum.
Authors: Huang, K. / Kapadia, G. / Zhu, P.P. / Peterkofsky, A. / Herzberg, O.
History
DepositionMay 19, 1998Processing site: BNL
Revision 1.0Aug 12, 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 / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 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: GLUCOSE-PERMEASE IIA COMPONENT


Theoretical massNumber of molelcules
Total (without water)16,7231
Polymers16,7231
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.330, 47.650, 71.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUCOSE-PERMEASE IIA COMPONENT


Mass: 16723.242 Da / Num. of mol.: 1 / Fragment: DOMAIN IIA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma capricolum (bacteria) / Strain: KID / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P45618, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20-30% PEG 3000, 0.3MM ZNCL2, 100MM TRIS-HCL BUFFER, PH 7.5.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-26 %PEG30001reservoir
20.3 mM1reservoirZnCl2
3100 mMTris-HCl1reservoir
410 mg/mlprotein1drop
510 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 4952 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rsym value: 0.069 / Net I/σ(I): 28.3
Reflection
*PLUS
Num. measured all: 12034 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.66 Å / % possible obs: 85.3 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.1

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5refinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPR

1gpr


Resolution: 2.5→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 2 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection% reflection
obs0.186 4296 87 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 134.2 Å2 / ksol: 0.6 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1176 0 0 62 1238
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.28
X-RAY DIFFRACTIONt_dihedral_angle_d20.2
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.02
X-RAY DIFFRACTIONt_gen_planes0.019
X-RAY DIFFRACTIONt_it2.6
X-RAY DIFFRACTIONt_nbd0.036
Software
*PLUS
Name: TNT / Version: V5.0 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.2
X-RAY DIFFRACTIONt_planar_d0.02
X-RAY DIFFRACTIONt_plane_restr0.019

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