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- PDB-1u7g: Crystal Structure of Ammonia Channel AmtB from E. Coli -

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Basic information

Entry
Database: PDB / ID: 1u7g
TitleCrystal Structure of Ammonia Channel AmtB from E. Coli
ComponentsProbable ammonium transporter
KeywordsTRANSPORT PROTEIN / Right handed helical bundle / transmembrane helices / Ammonia channnel / membrane protein / Rh protein
Function / homology
Function and homology information


ammonium transmembrane transport / ammonium transmembrane transporter activity / carbon dioxide transport / identical protein binding / plasma membrane
Similarity search - Function
Ammonium transporter, conserved site / Ammonium transporters signature. / Ammonium transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AMMONIA / AMMONIUM ION / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKhademi, S. / O'Connell III, J. / Remis, J. / Robles-Colmenares, Y. / Miercke, L.J.W. / Stroud, R.M.
CitationJournal: Science / Year: 2004
Title: Mechanism of ammonia transport by Amt/MEP/Rh: structure of AmtB at 1.35 A
Authors: Khademi, S. / O'Connell III, J. / Remis, J. / Robles-Colmenares, Y. / Miercke, L.J.W. / Stroud, R.M.
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7966
Polymers40,4351
Non-polymers3625
Water7,674426
1
A: Probable ammonium transporter
hetero molecules

A: Probable ammonium transporter
hetero molecules

A: Probable ammonium transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,38918
Polymers121,3053
Non-polymers1,08415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12050 Å2
ΔGint-134 kcal/mol
Surface area34990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.541, 96.541, 94.622
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21A-678-

HOH

31A-767-

HOH

DetailsThe biological assembly is a trimer.

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Components

#1: Protein Probable ammonium transporter


Mass: 40434.957 Da / Num. of mol.: 1 / Mutation: S68F,P126S,L255K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amtB / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / References: UniProt: P69681
#2: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#4: Chemical ChemComp-NH3 / AMMONIA / Ammonia


Mass: 17.031 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NH3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.96 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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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: Mar 14, 2004 / 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: 1.35→30 Å / Num. all: 109673 / Num. obs: 104957 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 1.6 / Num. unique all: 8850 / Rsym value: 0.621 / % possible all: 90.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U77

1u77


Resolution: 1.4→30 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.168 8731 -random
Rwork0.133 ---
all0.137 86836 --
obs0.137 86836 88.4 %-
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20.55 Å20 Å2
2--2.09 Å20 Å2
3----4.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2799 0 24 426 3249
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 1.4→1.49 Å /
Num. reflection% reflection
Rfree1207 -
obs11834 72.4 %

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