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- PDB-2b2f: Ammonium Transporter Amt-1 from A.fulgidus (Native) -

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Basic information

Entry
Database: PDB / ID: 2b2f
TitleAmmonium Transporter Amt-1 from A.fulgidus (Native)
Componentsammonium transporter
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN / TRANSPORTER
Function / homology
Function and homology information


ammonium channel activity / plasma membrane
Similarity search - Function
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
Ammonium transporter Amt1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAndrade, S.L. / Dickmanns, A. / Ficner, R. / Einsle, O.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Crystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus
Authors: Andrade, S.L. / Dickmanns, A. / Ficner, R. / Einsle, O.
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ammonium transporter


Theoretical massNumber of molelcules
Total (without water)42,0861
Polymers42,0861
Non-polymers00
Water2,684149
1
A: ammonium transporter

A: ammonium transporter

A: ammonium transporter


Theoretical massNumber of molelcules
Total (without water)126,2583
Polymers126,2583
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area11360 Å2
ΔGint-136 kcal/mol
Surface area32340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.308, 111.308, 136.563
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsTrimer, generated by the crystallographic threefold axis

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Components

#1: Protein ammonium transporter / amt-1


Mass: 42086.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: amt1 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): C43 / References: UniProt: O29285
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.97 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 400, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2005
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.72→100 Å / Num. all: 66323 / Num. obs: 67039 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.72→1.75 Å / % possible all: 90.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U77

1u77


Resolution: 1.72→35.2 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: THIS IS A TWINNED STRUCTURE. THE TWINNING OPERATOR IS (H,K,L) -> (H,-H-K,-L) AND THE TWINNING FRACTION IS 0.1135. THE R-FACTOR IS 0.181 AND THE R-FREE IS 0.20 WHEN THIS TWINNING OPERATOR IS USED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 3251 -RANDOM
Rwork0.1807 ---
obs0.1807 65969 98.4 %-
all-67039 --
Refinement stepCycle: LAST / Resolution: 1.72→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2895 0 0 149 3044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0064
X-RAY DIFFRACTIONc_angle_deg1.298

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