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- PDB-3c1h: Substrate binding, deprotonation and selectivity at the periplasm... -

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Basic information

Entry
Database: PDB / ID: 3c1h
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 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: 2.2 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: 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)44,7334
Polymers44,3761
Non-polymers3583
Water2,342130
1
A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,19912
Polymers133,1273
Non-polymers1,0739
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 area13200 Å2
ΔGint-122.6 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.175, 108.175, 84.663
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Ammonia channel / Ammonia transporter


Mass: 44375.617 Da / Num. of mol.: 1 / Mutation: F107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amtB / Plasmid: pET22b-AmtBF107A / 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-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 28% PEG 400, 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: 0.97934 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2006
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 28604 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.07 / Net I/σ(I): 15.41
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 2.52 / Rsym value: 0.57 / % possible all: 100

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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: 2.2→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 15.199 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.192 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23074 1447 5.1 %RANDOM
Rwork0.2042 ---
all0.20555 ---
obs0.20555 27078 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.101 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20.92 Å20 Å2
2--1.84 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 25 130 2796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222726
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9453714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.96923.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.861155
X-RAY DIFFRACTIONr_chiral_restr0.0850.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021984
X-RAY DIFFRACTIONr_nbd_refined0.2310.21768
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22007
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3170.2177
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.25
X-RAY DIFFRACTIONr_mcbond_it1.97721803
X-RAY DIFFRACTIONr_mcangle_it2.9832814
X-RAY DIFFRACTIONr_scbond_it5.044.51067
X-RAY DIFFRACTIONr_scangle_it6.1236899
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 110 -
Rwork0.356 1993 -
obs--99.95 %

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