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- PDB-3c1j: Substrate binding, deprotonation and selectivity at the periplasm... -

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Basic information

Entry
Database: PDB / ID: 3c1j
TitleSubstrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB
ComponentsAmmonia channel
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ammonia Transport / Phe-gate Double Mutant / AmtB / Inner membrane / Transmembrane'
Function / homology
Function and homology information


ammonium transmembrane transport / ammonium channel 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
ACETATE ION / IMIDAZOLE / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLupo, D. / Winkler, F.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Substrate binding, deprotonation, and selectivity at the periplasmic entrance of the Escherichia coli ammonia channel AmtB.
Authors: Javelle, A. / Lupo, D. / Ripoche, P. / Fulford, T. / Merrick, M. / Winkler, F.K.
History
DepositionJan 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5204
Polymers44,3001
Non-polymers2203
Water2,162120
1
A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,55912
Polymers132,8993
Non-polymers6619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12210 Å2
ΔGint-128.8 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.230, 110.230, 84.642
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-526-

HOH

21A-527-

HOH

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Components

#1: Protein Ammonia channel / Ammonia transporter


Mass: 44299.520 Da / Num. of mol.: 1 / Mutation: F107A, F215A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: 1amtB / Plasmid: pET22b-AmtBF107AF215A / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P69681
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 26% PEG 550, 0.1M sodium acetate, 0.2M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9998 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2006
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 38571 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.05 / Net I/σ(I): 17.74
Reflection shellResolution: 2→2.1 Å / Mean I/σ(I) obs: 3.44 / Rsym value: 0.47 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1XQF

1xqf


Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.089 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20974 1936 5 %RANDOM
Rwork0.18147 ---
all0.18285 ---
obs0.18285 36605 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 15 120 2771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222708
X-RAY DIFFRACTIONr_angle_refined_deg0.9991.9443690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7445361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.46823.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62115387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.505155
X-RAY DIFFRACTIONr_chiral_restr0.0720.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021971
X-RAY DIFFRACTIONr_nbd_refined0.1870.21458
X-RAY DIFFRACTIONr_nbtor_refined0.30.21970
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0980.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.219
X-RAY DIFFRACTIONr_mcbond_it2.30421814
X-RAY DIFFRACTIONr_mcangle_it3.04332816
X-RAY DIFFRACTIONr_scbond_it5.0744.51046
X-RAY DIFFRACTIONr_scangle_it6.4216874
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 142 -
Rwork0.264 2708 -
obs--99.86 %

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