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- PDB-5t12: N-terminal domain of Enzyme 1 - Nitrogen -

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Basic information

Entry
Database: PDB / ID: 5t12
TitleN-terminal domain of Enzyme 1 - Nitrogen
ComponentsPhosphoenolpyruvate--protein phosphotransferase
KeywordsTRANSFERASE / PTSNtr / phosphotransfer
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / response to organonitrogen compound / kinase activity / phosphorylation / metal ion binding / cytoplasm
Similarity search - Function
Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain ...Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily
Similarity search - Domain/homology
IODIDE ION / Phosphoenolpyruvate--protein phosphotransferase / Phosphoenolpyruvate-dependent phosphotransferase system
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsStanley, A.M. / Botos, I. / Buchanan, S.K.
CitationJournal: Structure / Year: 2016
Title: Structure of the NPr:EIN(Ntr) Complex: Mechanism for Specificity in Paralogous Phosphotransferase Systems.
Authors: Strickland, M. / Stanley, A.M. / Wang, G. / Botos, I. / Schwieters, C.D. / Buchanan, S.K. / Peterkofsky, A. / Tjandra, N.
History
DepositionAug 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate--protein phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9586
Polymers28,3231
Non-polymers6355
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-1 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.770, 64.770, 123.692
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Phosphoenolpyruvate--protein phosphotransferase / Phosphoenolpyruvate-protein phosphotransferase / Phosphoenolpyruvate-protein phosphotransferase PtsP


Mass: 28323.018 Da / Num. of mol.: 1 / Fragment: residues 170-424 / Mutation: H356Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ptsP, AC789_1c31510, ACU90_23270, AML37_15090, AWH59_07225, WQ89_09920
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0E1LBH7, UniProt: P37177*PLUS, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop
Details: 1.0M Potassium/Sodium tartrate 0.1M imidazole 8.0 0.2M NaCl 1.0M sodium iodide

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.299→33.221 Å / Num. obs: 11880 / % possible obs: 96.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.8
Reflection shellResolution: 2.299→2.38 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.48 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZYM

1zym


Resolution: 2.299→33.221 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.31
RfactorNum. reflection% reflection
Rfree0.2517 595 5.01 %
Rwork0.2133 --
obs0.2152 11880 90.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.299→33.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 5 43 1911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021894
X-RAY DIFFRACTIONf_angle_d0.5342569
X-RAY DIFFRACTIONf_dihedral_angle_d19.0321155
X-RAY DIFFRACTIONf_chiral_restr0.039294
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2993-2.53060.33461630.2862980X-RAY DIFFRACTION97
2.5306-2.89670.33711610.24683067X-RAY DIFFRACTION99
2.8967-3.64880.24481490.22252776X-RAY DIFFRACTION89
3.6488-33.22490.20031220.17762462X-RAY DIFFRACTION78

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