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- PDB-3c1g: Substrate binding, deprotonation and selectivity at the periplasm... -

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Basic information

Entry
Database: PDB / ID: 3c1g
TitleSubstrate binding, deprotonation and selectivity at the periplasmic entrance of the E. coli ammonia channel AmtB
ComponentsAmmonia channel
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ammonia Transport / wild-type 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 / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJavelle, A. / Kostrewa, D. / Lupo, 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 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7034
Polymers44,4521
Non-polymers2513
Water1,56787
1
A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules

A: Ammonia channel
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,10912
Polymers133,3553
Non-polymers7549
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 area11520 Å2
ΔGint-211.5 kcal/mol
Surface area33830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.329, 109.329, 84.821
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: 44451.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: amtB / Plasmid: pET22b-AmtB / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P69681
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.29 Å3/Da / Density % sol: 62.64 %
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: 0.9772 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2007
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 25706 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rsym value: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 2.48 / Rsym value: 0.48 / % possible all: 97.6

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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: 2.3→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.943 / SU B: 16.991 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24203 1300 5.1 %RANDOM
Rwork0.18507 ---
all0.18788 36372 --
obs0.18788 24136 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.155 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å21.03 Å20 Å2
2--2.06 Å20 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2648 0 14 87 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222721
X-RAY DIFFRACTIONr_angle_refined_deg1.191.9443710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2145361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01122.96381
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59215390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.378155
X-RAY DIFFRACTIONr_chiral_restr0.0820.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021976
X-RAY DIFFRACTIONr_nbd_refined0.230.21722
X-RAY DIFFRACTIONr_nbtor_refined0.3150.22002
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.23
X-RAY DIFFRACTIONr_mcbond_it1.90621806
X-RAY DIFFRACTIONr_mcangle_it2.97532819
X-RAY DIFFRACTIONr_scbond_it5.1074.51060
X-RAY DIFFRACTIONr_scangle_it6.0716891
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 100 -
Rwork0.305 1688 -
obs--97.28 %

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