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- PDB-9cs5: E. Coli AMTB with bound Xe ions -

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Basic information

Entry
Database: PDB / ID: 9cs5
TitleE. Coli AMTB with bound Xe ions
ComponentsAmmonium transporter AmtB
KeywordsMEMBRANE PROTEIN / Transport / channel / ammonia
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 AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter
Similarity search - Domain/homology
ACETIC ACID / AMINO GROUP / XENON / Ammonium transporter AmtB
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsVahedi-Faridi, A. / Kowatz, T. / Lodowski, D.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141612535, United States
CitationJournal: To Be Published
Title: E. Coli AMTB with bound Xe ions
Authors: Vahedi-Faridi, A. / Kowatz, T. / Lodowski, D.T.
History
DepositionJul 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ammonium transporter AmtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,58518
Polymers46,6671
Non-polymers1,91917
Water2,594144
1
A: Ammonium transporter AmtB
hetero molecules

A: Ammonium transporter AmtB
hetero molecules

A: Ammonium transporter AmtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,75654
Polymers140,0003
Non-polymers5,75651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15470 Å2
ΔGint-214 kcal/mol
Surface area34560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.343, 110.343, 84.457
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-507-

XE

21A-509-

XE

31A-510-

XE

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ammonium transporter AmtB / Ammonia channel AmtB / Ammonium channel AmtB


Mass: 46666.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: amtB, ybaG, b0451, JW0441 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P69681

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Non-polymers , 7 types, 161 molecules

#2: 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
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#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: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NH2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.18 Å3/Da / Density % sol: 61.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na-acetate, pH 4.6, 0.2 M MgSO4 and 23% PEG400
PH range: 4.6

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.000 , 1.4865
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 15, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.48651
ReflectionResolution: 2.13→95.56 Å / Num. obs: 32967 / % possible obs: 99.6 % / Redundancy: 9.9 % / Biso Wilson estimate: 40.76 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.034 / Net I/σ(I): 18.5
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 9.7 % / Num. unique obs: 2563 / CC1/2: 0.679 / Rpim(I) all: 0.562 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIXdev_5246refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→24.26 Å / SU ML: 0.2246 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1742 3333 5.19 %
Rwork0.1519 60876 -
obs0.1531 64209 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.97 Å2
Refinement stepCycle: LAST / Resolution: 2.13→24.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2707 0 48 144 2899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642855
X-RAY DIFFRACTIONf_angle_d0.69763896
X-RAY DIFFRACTIONf_chiral_restr0.0438463
X-RAY DIFFRACTIONf_plane_restr0.005477
X-RAY DIFFRACTIONf_dihedral_angle_d12.2425937
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.160.28931240.29412379X-RAY DIFFRACTION93.47
2.16-2.190.30981400.26652511X-RAY DIFFRACTION99.25
2.19-2.220.2571600.25122522X-RAY DIFFRACTION99.04
2.22-2.260.25331460.24942526X-RAY DIFFRACTION99.63
2.26-2.30.26881180.23172596X-RAY DIFFRACTION99.34
2.3-2.340.28061160.2232536X-RAY DIFFRACTION99.21
2.34-2.390.21731500.19612525X-RAY DIFFRACTION99.52
2.39-2.430.22151660.17482504X-RAY DIFFRACTION99.7
2.43-2.490.19521600.16312557X-RAY DIFFRACTION99.85
2.49-2.550.19681760.1572469X-RAY DIFFRACTION99.96
2.55-2.610.19421560.15512541X-RAY DIFFRACTION99.93
2.61-2.680.16381490.13012541X-RAY DIFFRACTION99.7
2.68-2.760.15911500.13292546X-RAY DIFFRACTION99.96
2.76-2.850.15181220.13062558X-RAY DIFFRACTION99.93
2.85-2.950.19311180.12672579X-RAY DIFFRACTION99.74
2.95-3.070.13061360.11132551X-RAY DIFFRACTION99.89
3.07-3.210.13651610.14152499X-RAY DIFFRACTION100
3.21-3.370.14021460.13652586X-RAY DIFFRACTION100
3.37-3.580.15671400.12382529X-RAY DIFFRACTION100
3.59-3.860.14321030.12542586X-RAY DIFFRACTION99.93
3.86-4.250.15281370.15422552X-RAY DIFFRACTION99.59
4.25-4.860.1364840.13442587X-RAY DIFFRACTION100
4.86-6.10.19761610.15752547X-RAY DIFFRACTION99.93
6.1-24.260.1871140.16312549X-RAY DIFFRACTION99.18
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.92458553186-0.2473439105470.002707875006962.50960522703-0.2094229279050.2878909861170.06295660205710.03275066221150.0902639737901-0.1217610639450.1376057754450.251249988314-0.335836999365-0.3038188347770.002046583006760.3434565370140.0207180339380.008831699495220.3418846160690.03046072212370.372295548103-9.5690565778572.036783925727.2769301916
22.554541141240.1319508695830.2984499324911.93792173742-0.1906857288511.801142225190.125389278503-0.04325133606950.21831690789-0.04681613617080.02741646093270.372549737726-0.184025991373-0.6408022123288.07689789358E-50.4066494260650.1089842067360.07088725986170.493733154340.06636314170450.46829615817-20.377321981675.481800420432.595970329
31.57449648022-0.0608135640136-0.3596939500721.727968708350.3121087468211.310236028470.0685178649610.124255233308-0.0814371365740.01532292559740.04920949697990.1793409340940.172369623663-0.43895430485-5.94362705825E-50.298714938837-0.0786229676422-0.03897979792460.4087700971390.05321982503550.367375713508-16.338670324953.880528177226.7777689708
42.59700440742-0.521217124478-0.02708173377863.018707956211.211108887770.4997071726860.1839451117110.1530413714430.0180548128739-0.171529976714-0.0822796636870.1269399882660.299708965303-0.4919082967830.001243218947730.352467987822-0.0793711837821-0.02065839373370.6359020668220.08132445470170.564249559794-27.231584201156.914335837131.9014784268
51.991531243040.6641573481340.2821441106022.869213311740.04191535759961.611201634280.06441615392270.2963355643850.275634342339-0.4801610083250.09447843070840.440425023101-0.153350227774-0.8072081248190.03853711866430.3052400285870.175862609887-0.01402716087410.7063590960230.09743822180430.447980602522-30.818528627173.377722158124.9531526804
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 61 )1 - 611 - 61
22chain 'A' and (resid 62 through 197 )62 - 19762 - 187
33chain 'A' and (resid 198 through 301 )198 - 301188 - 291
44chain 'A' and (resid 302 through 347 )302 - 347292 - 332
55chain 'A' and (resid 348 through 387 )348 - 387333 - 372

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