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- PDB-2a0j: Crystal Structure of Nitrogen Regulatory Protein IIA-Ntr from Nei... -

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Basic information

Entry
Database: PDB / ID: 2a0j
TitleCrystal Structure of Nitrogen Regulatory Protein IIA-Ntr from Neisseria meningitidis
ComponentsPTS system, nitrogen regulatory IIA protein
KeywordsTRANSFERASE / nitrogen regulation / Structural Genomics / OPPF / Oxford Protein Production Facility
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / protein kinase activator activity
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
PTS system, nitrogen regulatory IIA protein
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRen, J. / Sainsbury, S. / Berrow, N.S. / Alderton, D. / Nettleship, J.E. / Stammers, D.K. / Saunders, N.J. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: Bmc Struct.Biol. / Year: 2005
Title: Crystal structure of nitrogen regulatory protein IIANtr from Neisseria meningitidis
Authors: Ren, J. / Sainsbury, S. / Berrow, N.S. / Alderton, D. / Nettleship, J.E. / Stammers, D.K. / Saunders, N.J. / Owens, R.J.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PTS system, nitrogen regulatory IIA protein


Theoretical massNumber of molelcules
Total (without water)16,1131
Polymers16,1131
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.020, 61.020, 63.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PTS system, nitrogen regulatory IIA protein


Mass: 16112.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: ptsN / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)
References: UniProt: Q9K082, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.11 Å3/Da / Density % sol: 41.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 3.2 M ammonium sulphate, 0.1 M citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.945 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.945 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 4988 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 7.6 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.183 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.9 / Num. unique all: 486 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→27.49 Å / Rfactor Rfree error: 0.017 / Data cutoff high absF: 1257584.73 / Data cutoff high rms absF: 1257584.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 270 5.4 %RANDOM
Rwork0.201 ---
obs0.201 4973 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.7357 Å2 / ksol: 0.390587 e/Å3
Displacement parametersBiso mean: 27.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å21.76 Å20 Å2
2--0.77 Å20 Å2
3----1.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1104 0 0 46 1150
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.234
X-RAY DIFFRACTIONc_mcangle_it5.98
X-RAY DIFFRACTIONc_scbond_it9.146
X-RAY DIFFRACTIONc_scangle_it11.9112
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.072 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.353 24 4.9 %
Rwork0.291 461 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top

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