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- PDB-4gqx: Crystal structure of EIIA(NTR) from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 4gqx
TitleCrystal structure of EIIA(NTR) from Burkholderia pseudomallei
ComponentsPTS IIA-like nitrogen-regulatory protein PtsN
KeywordsTRANSFERASE / EIIA(NTR) / alpha/beta / histidine containing phosphocarrier protein / NPR / EI(NTR) / NA
Function / homology
Function and homology information


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 IIA-like nitrogen-regulatory protein PtsN
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKim, M.-S. / Shin, D.H.
CitationJournal: Proteins / Year: 2013
Title: New molecular interaction of IIA(Ntr) and HPr from Burkholderia pseudomallei identified by X-ray crystallography and docking studies
Authors: Kim, M.-S. / Lee, H. / Heo, L. / Lim, A. / Seok, C. / Shin, D.H.
History
DepositionAug 24, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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:
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Assembly

Deposited unit
A: PTS IIA-like nitrogen-regulatory protein PtsN
B: PTS IIA-like nitrogen-regulatory protein PtsN


Theoretical massNumber of molelcules
Total (without water)36,2972
Polymers36,2972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-5 kcal/mol
Surface area13320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.203, 67.203, 144.104
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 PTS IIA-like nitrogen-regulatory protein PtsN / EIIA


Mass: 18148.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: ptsN / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JW77

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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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 10% PEG 1K, 8% PEG 8K, 0.1M Sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 5, 2010
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 7428 / Num. obs: 7353 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellHighest resolution: 3 Å / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 46936.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 742 10.8 %RANDOM
Rwork0.234 ---
all0.2371 7428 --
obs0.234 6840 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.4993 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 57.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.71 Å20 Å20 Å2
2--8.71 Å20 Å2
3----17.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a1.03 Å0.71 Å
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2384 0 0 0 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_mcbond_it10.511.5
X-RAY DIFFRACTIONc_mcangle_it16.392
X-RAY DIFFRACTIONc_scbond_it12.792
X-RAY DIFFRACTIONc_scangle_it18.362.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.046 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.473 107 10.7 %
Rwork0.392 892 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

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