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- PDB-3urr: Structure of PTS IIA-like nitrogen-regulatory protein PtsN (BTH_I... -

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Basic information

Entry
Database: PDB / ID: 3urr
TitleStructure of PTS IIA-like nitrogen-regulatory protein PtsN (BTH_I0484) (ptsN)
ComponentsPTS IIA-like nitrogen-regulatory protein PtsN
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system
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
PHOSPHATE ION / PTS IIA-like nitrogen-regulatory protein PtsN
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.397 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionNov 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: PTS IIA-like nitrogen-regulatory protein PtsN
B: PTS IIA-like nitrogen-regulatory protein PtsN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3506
Polymers33,9792
Non-polymers3714
Water5,621312
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-20 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.975, 102.267, 37.477
Angle α, β, γ (deg.)90.000, 92.890, 90.000
Int Tables number4
Space group name H-MP1211
DetailsBIOLOGICAL ASSEMBLY IS UNKNOWN AS PER THE AUTHORS

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Components

#1: Protein PTS IIA-like nitrogen-regulatory protein PtsN


Mass: 16989.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0484, ptsN / Plasmid: Ava0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T1A8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2 M Lithium Sulfate, 0.1 M sodium acetate pH 4.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.397→50 Å / Num. obs: 54470 / % possible obs: 99.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.075 / Χ2: 0.996 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.397-1.453.90.56954400.944199.6
1.45-1.5140.40154531.0121100
1.51-1.5840.2854110.9921100
1.58-1.664.10.21254531.0031100
1.66-1.764.10.16354770.9831100
1.76-1.94.10.12354140.9961100
1.9-2.094.10.154721.033199.9
2.09-2.394.10.09654461.0171100
2.39-3.024.20.07954911.033199.8
3.02-504.10.06254130.94198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A0J

2a0j


Resolution: 1.397→35.149 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8392 / SU ML: 0.43 / σ(F): 1.35 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 2756 5.06 %RANDOM
Rwork0.17 ---
obs0.1716 54434 99.16 %-
all-54434 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.776 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso max: 117.06 Å2 / Biso mean: 26.97 Å2 / Biso min: 13.18 Å2
Baniso -1Baniso -2Baniso -3
1--1.0715 Å20 Å2-0.6784 Å2
2---4.8407 Å2-0 Å2
3---5.9122 Å2
Refinement stepCycle: LAST / Resolution: 1.397→35.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 23 312 2652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082453
X-RAY DIFFRACTIONf_angle_d1.2133354
X-RAY DIFFRACTIONf_chiral_restr0.07400
X-RAY DIFFRACTIONf_plane_restr0.005439
X-RAY DIFFRACTIONf_dihedral_angle_d12.29926
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.397-1.42140.36691370.34942304244188
1.4214-1.44720.34441250.316625722697100
1.4472-1.47510.34051270.282826182745100
1.4751-1.50520.26171350.259926222757100
1.5052-1.53790.29991340.253625852719100
1.5379-1.57370.27651400.229925732713100
1.5737-1.6130.27091290.226226272756100
1.613-1.65660.2391320.206325932725100
1.6566-1.70540.25041430.211926342777100
1.7054-1.76040.26451300.201326022732100
1.7604-1.82330.23581520.188925552707100
1.8233-1.89630.20781330.172426192752100
1.8963-1.98260.18331410.158726152756100
1.9826-2.08710.19621550.158125892744100
2.0871-2.21790.19061220.154826252747100
2.2179-2.38910.20521590.160125512710100
2.3891-2.62950.22681400.159826302770100
2.6295-3.00980.2011410.160126012742100
3.0098-3.79130.16691520.151225952747100
3.7913-35.16010.1771290.15652568269797
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1291-0.1606-0.19564.076-1.5843.54450.09980.2102-0.04110.0122-0.2103-0.09240.3210.14450.09370.3274-0.0102-0.01570.1865-0.00630.0762-1.406543.684513.9294
28.17970.81830.34474.9311-2.29193.8573-0.174-0.1291-0.68310.1974-0.2234-0.57311.37580.49260.22530.39150.05480.04290.14690.01960.200310.234440.444320.4569
37.04112.89132.62038.52193.97245.16730.28060.57360.1464-0.413-0.04290.2095-0.48520.1061-0.07070.23470.09290.0420.28140.06220.14114.61547.169718.7912
41.62870.5595-0.18571.4191-0.44823.7375-0.013-0.05030.06550.049-0.0039-00.10480.28480.0240.25880.02520.00690.1783-0.00050.05724.814648.86221.4335
50.8803-0.01210.18290.41480.17514.1370.0508-0.1516-0.10770.1718-0.0026-0.00580.50180.2340.07970.45270.0228-0.00140.20610.02230.06040.86142.980332.3307
61.69350.4859-0.04671.92640.14641.9418-0.0037-0.0473-0.07370.0014-0.01760.12120.1121-0.19530.02890.29040.01530.00260.18920.00380.0541-5.860949.021818.0016
76.1155-0.7199-2.96921.80821.71024.30010.1984-0.44660.20620.532-0.0396-0.1415-0.09180.1906-0.14930.354-0.0541-0.03310.2-0.01230.10263.533770.739433.5154
81.89111.55740.64871.7902-1.00994.91690.0731-0.12180.32390.27570.05640.2963-0.4917-0.3104-0.12430.39090.07930.06870.16660.0080.1304-11.623376.726828.1191
90.74440.30060.1081.4858-0.37592.2848-0.03460.03760.0657-0.1240.0064-0.0254-0.1618-0.05690.01860.32750.02050.01570.15270.00740.0494-6.65371.15522.319
108.78820.7539-0.75016.45443.43815.5049-0.13520.46120.3362-0.5901-0.06360.4513-0.3114-0.15620.19690.223-0.0044-0.02780.24150.00990.1172-18.99762.021627.8133
110.8137-0.1364-0.01781.0805-0.17721.25330.0978-0.15880.05910.2510.0189-0.033-0.19270.046-0.06920.3754-0.0066-0.00050.1687-0.0068-0.0137-2.004964.081332.9685
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 0:20)B0 - 20
2X-RAY DIFFRACTION2(chain B and resid 21:34)B21 - 34
3X-RAY DIFFRACTION3(chain B and resid 35:51)B35 - 51
4X-RAY DIFFRACTION4(chain B and resid 52:84)B52 - 84
5X-RAY DIFFRACTION5(chain B and resid 85:100)B85 - 100
6X-RAY DIFFRACTION6(chain B and resid 101:151)B101 - 151
7X-RAY DIFFRACTION7(chain A and resid 0:13)A0 - 13
8X-RAY DIFFRACTION8(chain A and resid 14:36)A14 - 36
9X-RAY DIFFRACTION9(chain A and resid 37:84)A37 - 84
10X-RAY DIFFRACTION10(chain A and resid 85:96)A85 - 96
11X-RAY DIFFRACTION11(chain A and resid 97:151)A97 - 151

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