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- PDB-2ns1: Crystal structure of the e. coli ammonia channel AMTB complexed w... -

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Basic information

Entry
Database: PDB / ID: 2ns1
TitleCrystal structure of the e. coli ammonia channel AMTB complexed with the signal transduction protein GLNK
Components
  • Ammonia channel
  • Nitrogen regulatory protein P-II 2
KeywordsTRANSPORT PROTEIN/SIGNALING PROTEIN / PROTEIN-PROTEIN COMPLEX / MEMBRANE PROTEIN / AMMONIA / CHANNEL / REGULATORY / INHIBITOR / SIGNAL PROTEIN / ADP / BOG / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / TRANSPORT PROTEIN-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of nitrogen utilization / ammonium transmembrane transport / ammonium transmembrane transporter 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. / Ammonium transporter / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter ...Ammonium transporter, conserved site / Ammonium transporters signature. / Ammonium transporter / Nitrogen regulatory protein P-II, urydylation site / P-II protein uridylation site. / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Nitrogen regulatory protein PII, conserved site / P-II protein C-terminal region signature. / Nitrogen regulatory protein P-II / Nitrogen regulatory protein P-II / 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: 1.962 Å
AuthorsGruswitz, F. / O'Connell III, J. / Stroud, R.M. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Inhibitory complex of the transmembrane ammonia channel, AmtB, and the cytosolic regulatory protein, GlnK, at 1.96
Authors: Gruswitz, F. / O'Connell III, J. / Stroud, R.M.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN Water residues 501-572 represent partial density for detergent

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonia channel
B: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,52113
Polymers55,5112
Non-polymers3,01011
Water8,971498
1
A: Ammonia channel
B: Nitrogen regulatory protein P-II 2
hetero molecules

A: Ammonia channel
B: Nitrogen regulatory protein P-II 2
hetero molecules

A: Ammonia channel
B: Nitrogen regulatory protein P-II 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,56439
Polymers166,5326
Non-polymers9,03133
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area38010 Å2
ΔGint-91 kcal/mol
Surface area46840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.032, 102.032, 363.849
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

21A-921-

HOH

31A-955-

HOH

41B-262-

HOH

51B-263-

HOH

DetailsThe biological assembly is two trimers generated from the heterodimer in the asymmetric unit by the operations: x,y,z and -y, x-y, z and -x+y, -x, z.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ammonia channel / Ammonia transporter


Mass: 42952.285 Da / Num. of mol.: 1 / Fragment: Residues 23-428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: amtB / Plasmid: PET29B / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: P69681
#2: Protein Nitrogen regulatory protein P-II 2


Mass: 12558.488 Da / Num. of mol.: 1 / Mutation: Y51F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glnK / Plasmid: PET47B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AC55

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Sugars , 1 types, 8 molecules

#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 501 molecules

#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 3.28 Å3/Da / Density % sol: 62.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 550MME, 0.12M TRIS(HYDROXYMETHYL)AMINOMETHANE, 2mM ADENOSINE-5'-TRIPHOSPHATE, 25mM AMONIUM SULFATE, 0.04M B-OCTYLGLUCOSIDE, 2mM DITHIOTHREITOL, 0.05M SODIUM CHLORIDE, pH 8.0, VAPOR ...Details: 20% PEG 550MME, 0.12M TRIS(HYDROXYMETHYL)AMINOMETHANE, 2mM ADENOSINE-5'-TRIPHOSPHATE, 25mM AMONIUM SULFATE, 0.04M B-OCTYLGLUCOSIDE, 2mM DITHIOTHREITOL, 0.05M SODIUM CHLORIDE, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2006 / Details: SI(111)
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.962→43.07 Å / Num. all: 53722 / Num. obs: 52357 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 32.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 41.2
Reflection shellResolution: 1.962→2.03 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4864 / Rsym value: 0.611 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U7G and PDB ENTRY 2GNK

1u7g

2gnk


Resolution: 1.962→43.07 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.799 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19838 2562 5 %RANDOM
Rwork0.16248 ---
obs0.16435 48839 97.47 %-
all-48839 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.533 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.962→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 203 498 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224214
X-RAY DIFFRACTIONr_bond_other_d0.0020.022801
X-RAY DIFFRACTIONr_angle_refined_deg1.4842.0015734
X-RAY DIFFRACTIONr_angle_other_deg1.4936884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13923.472144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04215647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0371517
X-RAY DIFFRACTIONr_chiral_restr0.2240.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_nbd_refined0.2070.2990
X-RAY DIFFRACTIONr_nbd_other0.1840.22904
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22149
X-RAY DIFFRACTIONr_nbtor_other0.0860.22093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2366
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0170.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.259
X-RAY DIFFRACTIONr_mcbond_it4.45823354
X-RAY DIFFRACTIONr_mcbond_other1.26121105
X-RAY DIFFRACTIONr_mcangle_it4.87934133
X-RAY DIFFRACTIONr_scbond_it4.35921898
X-RAY DIFFRACTIONr_scangle_it5.7431586
LS refinement shellResolution: 1.962→2.013 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 157 -
Rwork0.207 3428 -
obs--92.78 %

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