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PDB | 2B2J | Ammonium Transporter Amt-1 from A. fulgidus (Xe)

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Internal ID
31907
PDB Entry ID
2B2J
Title
Ammonium Transporter Amt-1 from A. fulgidus (Xe)
Authors
Andrade, S.L.A.,Dickmanns, A.,Ficner, R.,Einsle, O.
Primary Citation
AuthorsAndrade, S.L., Dickmanns, A., Ficner, R., Einsle, O.
TitleCrystal structure of the archaeal ammonium transporter Amt-1 from Archaeoglobus fulgidus
JournalProc.Natl.Acad.Sci.Usa, v.102, pp.14994 - 14999, 2005
AbstractView
Pubmed16214888
DOI10.1073/pnas.0506254102
 
History
Deposition: 2005-09-19Release: 2005-10-11Last Modified: 2011-07-13
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.850.1970.1970.221H 3
Unit Cell
Length [Å]a111.46b111.46c135.58
Angles [°]alpha90.00beta90.00gamma120.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1ammonium transporterA
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Archaeoglobus fulgidusEscherichia coli
Related PDB Entries
IDDetails
2B2FNative Structure
2B2HAmmonium Transporter Amt-1 (AS)
2B2IAmmonium Transporter Amt-1 (MA)
Chemical Component
IdentifierNameFromulaLigand StructureLigand Interaction
XEXENONXe[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTransport Protein
TextMEMBRANE PROTEIN, TRANSPORTER, Transport Protein
 
Polymeric Molecules
Chain A
Descriptionammonium transporter
Polymer typepolypeptide
Formula Weight42086.5
Source Methodgenetically manipulated
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aApolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
XEXENONXe131.300View
Natural/Genetically Modified Source
Scientific NameArchaeoglobus fulgidus
Source GenusArchaeoglobus
Geneamt1
Host Common Namen/a
Host Scientific NameEscherichia coli
Host GenusEscherichia coli
Host Cell Linen/a
Host StrainC43
Host Vector Typeplasmid
Host PlasmidpET
 
Crystallization Experiments
MethodVAPOR DIFFUSION, SITTING DROP
PH8.5
Temperature298.0
DetailsPEG 400, Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
111.46111.46135.58
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.00120.00
Space Group
H 3
Diffraction Detector
DetectorIMAGE PLATE
TypeMARRESEARCH
Detailsn/a
Collection Date2005-05-17
 
Diffraction Radiation
MonochromatorRIGAKU MIRRORS
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List1.5418
 
Diffraction Source
SourceROTATING ANODE
TypeRIGAKU
Siten/a
Beamlinen/a
 
Reflection Details
Observed Criterion Sigma (F)2.0
Observed Criterion Sigma (I)2.0
Resolution (High)1.85
Resolution (Low)100.00
Number Reflections (All) 53626
Number Reflections (Observed)52810
Percent Possible (Observed)98.6
R Merge I (Observed)n/a
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancyn/a
 
High Resolution Shell Details
Resolution(High)1.85
Resolution(Low)1.95
Percent Possible(All) 91.50
R Merge I(Observed)n/a
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancyn/a
Num Unique Reflections(All)n/a
 
Refinement Statistics
Structure Solution MethodMOLECULAR REPLACEMENT
Resolution (High)1.85
Resolution (Low)100.00
Cut-off Sigma (F)2.0
Cut-off Sigma (I)n/a
Number of Reflections (All)53626
Number of Reflections (Observed)52478
Number of Reflections (R-Free) 2529
Percent Reflections (Observed)n/a
R-Factor (All)n/a
R-Factor (Observed)0.197
R-Work0.197
R-Free0.221
R-Free Selection DetailsRANDOM
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Valuen/a
Anisotropic B[1][1]n/a
Anisotropic B[1][2]n/a
Anisotropic B[1][3]n/a
Anisotropic B[2][2]n/a
Anisotropic B[2][3]n/a
Anisotropic B[3][3]n/a
 
RMS Deviations
Parameter TypeDeviation From Ideal
c_bond_d0.0069
c_angle_deg1.240
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms2895
Nucleic Acid Atoms0
Heterogen Atoms15
Solvent Atoms106
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)DENZO
Data Reduction (data scaling)SCALEPACK
Structure SolutionMOLREP
Structure RefinementCNS 1.1
 
Software
Classificationdata collection
Software NameDENZO
 
Classificationdata reduction
Software NameSCALEPACK
 
Classificationmodel building
Software NameMOLREP
 
Classificationrefinement
Software NameCNS
Software Version 1.1
 
Sequence Chain
A
Sequence
  1   MSDGNVAWIL  ASTALVMLMV  PGVGFFYAGM  VRRKNAVNMI  ALSFISLIIT  VLLWIFYGYS

 61   VSFGNDISGI  IGGLNYALLS  GVKGEDLLFM  MYQMMFAAVT  IAILTSAIAE  RAKVSSFILL

121   SALWLTFVYA  PFAHWLWGGG  WLAKLGALDF  AGGMVVHISS  GFAALAVAMT  IGKRAGFEEY

181   SIEPHSIPLT  LIGAALLWFG  WFGFNGGSAL  AANDVAINAV  VVTNTSAAVA  GFVWMVIGWI

241   KGKPGSLGIV  SGAIAGLAAI  TPAAGFVDVK  GAIVIGLVAG  IVCYLAMDFR  IKKKIDESLD

301   AWAIHGIGGL  WGSVAVGILA  NPEVNGYAGL  LFGNPQLLVS  QLIAVASTTA  YAFLVTLILA

361   KAVDAAVGLR  VSSQEEYVGL  DLSQHEEVAY  TLEHHHHHH