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Basic information

Entry
Database: PDB / ID: 2nuu
TitleRegulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex
Components
  • Ammonia channel
  • Nitrogen regulatory protein P-II 2
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / Membrane protein complex / nitrogen regulation / ammonia transport / TRANSPORT PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of nitrogen utilization / ammonium transmembrane transport / ammonium channel activity / regulation of nitrogen utilization / enzyme regulator activity / carbon dioxide transport / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Ammonium transporter, conserved site / Ammonium transporters signature. / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Ammonium transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Nitrogen regulatory protein PII, conserved site ...Ammonium transporter, conserved site / Ammonium transporters signature. / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Ammonium transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / Ammonium/urea transporter / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nitrogen regulatory protein GlnK / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsConroy, M.J. / Durand, A. / Lupo, D. / Li, X.-D. / Bullough, P.A. / Winkler, F.K. / Merrick, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: The crystal structure of the Escherichia coli AmtB-GlnK complex reveals how GlnK regulates the ammonia channel
Authors: Conroy, M.J. / Durand, A. / Lupo, D. / Li, X.-D. / Bullough, P.A. / Winkler, F.K. / Merrick, M.
History
DepositionNov 9, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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: Ammonia channel
B: Ammonia channel
C: Ammonia channel
D: Ammonia channel
E: Ammonia channel
F: Ammonia channel
G: Nitrogen regulatory protein P-II 2
H: Nitrogen regulatory protein P-II 2
I: Nitrogen regulatory protein P-II 2
J: Nitrogen regulatory protein P-II 2
K: Nitrogen regulatory protein P-II 2
L: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,60718
Polymers334,04312
Non-polymers2,5636
Water9,908550
1
A: Ammonia channel
B: Ammonia channel
C: Ammonia channel
G: Nitrogen regulatory protein P-II 2
H: Nitrogen regulatory protein P-II 2
I: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3039
Polymers167,0226
Non-polymers1,2823
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27650 Å2
ΔGint-200 kcal/mol
Surface area46110 Å2
MethodPISA
2
D: Ammonia channel
E: Ammonia channel
F: Ammonia channel
J: Nitrogen regulatory protein P-II 2
K: Nitrogen regulatory protein P-II 2
L: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,3039
Polymers167,0226
Non-polymers1,2823
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27460 Å2
ΔGint-206 kcal/mol
Surface area46350 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area59770 Å2
ΔGint-428 kcal/mol
Surface area87800 Å2
MethodPISA
4
A: Ammonia channel
B: Ammonia channel
C: Ammonia channel
G: Nitrogen regulatory protein P-II 2
H: Nitrogen regulatory protein P-II 2
I: Nitrogen regulatory protein P-II 2
hetero molecules

D: Ammonia channel
E: Ammonia channel
F: Ammonia channel
J: Nitrogen regulatory protein P-II 2
K: Nitrogen regulatory protein P-II 2
L: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,60718
Polymers334,04312
Non-polymers2,5636
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area56980 Å2
ΔGint-405 kcal/mol
Surface area90590 Å2
MethodPISA
5
A: Ammonia channel
B: Ammonia channel
C: Ammonia channel
G: Nitrogen regulatory protein P-II 2
H: Nitrogen regulatory protein P-II 2
I: Nitrogen regulatory protein P-II 2
hetero molecules

D: Ammonia channel
E: Ammonia channel
F: Ammonia channel
J: Nitrogen regulatory protein P-II 2
K: Nitrogen regulatory protein P-II 2
L: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,60718
Polymers334,04312
Non-polymers2,5636
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area56610 Å2
ΔGint-424 kcal/mol
Surface area90960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.691, 107.865, 280.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ammonia channel / Ammonia transporter / AmtB


Mass: 43397.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GT1000 / Gene: amtB / Plasmid: pAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): GT1000 / References: UniProt: P69681
#2: Protein
Nitrogen regulatory protein P-II 2 / GlnK


Mass: 12276.192 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: GT1000 / Gene: glnK / Plasmid: pAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): GT1000 / References: UniProt: P0AC55
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 65% MPD, 100mM Tris pH8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97972 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 14, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97972 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 105009 / Redundancy: 4.17 % / Rsym value: 0.0989 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.21 % / Mean I/σ(I) obs: 3 / Rsym value: 0.536

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1U7G

1u7g


Resolution: 2.5→40 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.909 / SU B: 21.864 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 1.121 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24942 5272 5 %RANDOM
Rwork0.1712 ---
obs0.17506 99734 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.201 Å2
Baniso -1Baniso -2Baniso -3
1--1.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23314 0 162 550 24026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02223975
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.95532601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.72953115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61923.423859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.324153745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0361590
X-RAY DIFFRACTIONr_chiral_restr0.1050.23829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220711
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.212416
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.216803
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2965
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.149215619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.687324362
X-RAY DIFFRACTIONr_scbond_it7.694.59554
X-RAY DIFFRACTIONr_scangle_it9.75468239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 415 -
Rwork0.236 7244 -
obs--99.83 %

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