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- PDB-1a6j: NITROGEN REGULATORY BACTERIAL PROTEIN IIA-NITROGEN -

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Basic information

Entry
Database: PDB / ID: 1a6j
TitleNITROGEN REGULATORY BACTERIAL PROTEIN IIA-NITROGEN
ComponentsNITROGEN REGULATORY IIA PROTEIN
KeywordsPHOSPHOTRANSFERASE SYSTEM / NITROGEN REGULATION
Function / homology
Function and homology information


regulation of monoatomic ion transmembrane transporter activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / enzyme inhibitor activity / protein kinase activator activity / response to organonitrogen compound / kinase activity / cytosol
Similarity search - Function
Phosphotransferase system, IIA-like nitrogen-regulatory protein PtsN / PTS EIIA domains phosphorylation site signature 2. / PTS EIIA type-2 domain / Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2 / PTS_EIIA type-2 domain profile. / Mannitol-specific EII; Chain A / Mannitol-specific EII; Chain A / Phosphotransferase/anion transporter / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Nitrogen regulatory protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.35 Å
AuthorsBordo, D. / Van Montfort, R. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier, M.H. / Dijkstra, B.W.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The three-dimensional structure of the nitrogen regulatory protein IIANtr from Escherichia coli.
Authors: Bordo, D. / van Monfort, R.L. / Pijning, T. / Kalk, K.H. / Reizer, J. / Saier Jr., M.H. / Dijkstra, B.W.
History
DepositionFeb 25, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NITROGEN REGULATORY IIA PROTEIN
B: NITROGEN REGULATORY IIA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2155
Polymers35,9632
Non-polymers2523
Water1,17165
1
A: NITROGEN REGULATORY IIA PROTEIN
B: NITROGEN REGULATORY IIA PROTEIN
hetero molecules

A: NITROGEN REGULATORY IIA PROTEIN
B: NITROGEN REGULATORY IIA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,43110
Polymers71,9264
Non-polymers5056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8490 Å2
ΔGint-78 kcal/mol
Surface area24680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.900, 107.900, 64.300
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 NITROGEN REGULATORY IIA PROTEIN / IIA-NITROGEN / ENZYME IIA-NTR


Mass: 17981.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12/W3110 / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P69829, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7.5
Details: PROTEIN CRYSTALLIZED WITH THE HANGING DROP SETUP. RESERVOIR CONTAINING 1.8 M AMMONIUM SULPHATE, 1 MM SODIUM AZIDE, 2MM DTT AND 0.1 M BES-NAOH, PH 7.5.
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mg/mlprotein1drop
20.9-1.0 Mammonium sulfate1drop
30.5 mM1dropNaN3
41 mMdithiothreitol1drop
50.05 MBes-NaOH1drop
61.8-2.0 Mammonium sulfate1reservoir
71 mM1reservoirNaN3
82 mMdithiothreitol1reservoir
90.1 MBes-NaOH1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 15, 1995
RadiationMonochromator: CU / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 14482 / % possible obs: 89 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 14
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 5 / Rsym value: 0.2 / % possible all: 75
Reflection
*PLUS
Num. measured all: 104938
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.2

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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: MIR / Resolution: 2.35→40 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1470 9.7 %RANDOM
Rwork0.197 ---
obs0.197 14482 89 %-
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 13 65 2461
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.58
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
LS refinement shellResolution: 2.35→2.46 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.33 50 11.28 %
Rwork0.28 1329 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19.WATTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPH19.SOL

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