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- PDB-6csf: Crystal structure of sodium/alanine symporter AgcS with D-alanine... -

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Basic information

Entry
Database: PDB / ID: 6csf
TitleCrystal structure of sodium/alanine symporter AgcS with D-alanine bound
Components
  • Monoclonal antibody FAB heavy chain
  • Monoclonal antibody FAB light chain
  • Sodium/alanine symporter AgcS
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


amino acid:sodium symporter activity / plasma membrane
Similarity search - Function
Sodium:alanine symporter / Sodium:alanine symporter family / Sodium:alanine symporter family signature. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
D-ALANINE / Sodium/alanine symporter AgcS
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å
AuthorsMa, J. / Reyes, F.E. / Gonen, T.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Structural basis for substrate binding and specificity of a sodium-alanine symporter AgcS.
Authors: Ma, J. / Lei, H.T. / Reyes, F.E. / Sanchez-Martinez, S. / Sarhan, M.F. / Hattne, J. / Gonen, T.
History
DepositionMar 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monoclonal antibody FAB heavy chain
B: Monoclonal antibody FAB light chain
M: Sodium/alanine symporter AgcS
H: Monoclonal antibody FAB heavy chain
C: Sodium/alanine symporter AgcS
L: Monoclonal antibody FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,4438
Polymers185,3316
Non-polymers1122
Water0
1
A: Monoclonal antibody FAB heavy chain
B: Monoclonal antibody FAB light chain
C: Sodium/alanine symporter AgcS


Theoretical massNumber of molelcules
Total (without water)92,6663
Polymers92,6663
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-34 kcal/mol
Surface area34820 Å2
MethodPISA
2
M: Sodium/alanine symporter AgcS
H: Monoclonal antibody FAB heavy chain
L: Monoclonal antibody FAB light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7785
Polymers92,6663
Non-polymers1122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-37 kcal/mol
Surface area34630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.051, 183.051, 349.843
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain H
12chain M
22chain C
13chain B
23chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 224
211chain HH1 - 224
112(chain G and resid 16 through 448)M16 - 448
212(chain J and (resid 16 through 52 or resid 56 through 448))C16 - 52
222(chain J and (resid 16 through 52 or resid 56 through 448))C56 - 448
113chain BB1 - 213
213chain LL1 - 213

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Monoclonal antibody FAB heavy chain


Mass: 22220.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Monoclonal antibody FAB light chain


Mass: 22891.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Sodium/alanine symporter AgcS / Alanine permease


Mass: 47553.504 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (strain S2 / LL) (archaea)
Strain: S2 / LL / Gene: agcS, MMP1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LX42
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 2.5M Ammonium Sulfate, 100mM Sodium Citrate pH 5.0-5.5

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.3→158.53 Å / Num. obs: 99301 / % possible obs: 99.9 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rpim(I) all: 0.099 / Net I/σ(I): 6.9
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4881 / CC1/2: 0.354 / Rpim(I) all: 0.766 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 3.3→158.527 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.37
RfactorNum. reflection% reflection
Rfree0.2533 4919 4.96 %
Rwork0.2396 --
obs0.2403 99144 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 247.02 Å2 / Biso mean: 117.5076 Å2 / Biso min: 45.18 Å2
Refinement stepCycle: final / Resolution: 3.3→158.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12663 0 7 0 12670
Biso mean--129.07 --
Num. residues----1713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412999
X-RAY DIFFRACTIONf_angle_d0.817691
X-RAY DIFFRACTIONf_chiral_restr0.052072
X-RAY DIFFRACTIONf_plane_restr0.0052211
X-RAY DIFFRACTIONf_dihedral_angle_d4.5667522
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1868X-RAY DIFFRACTION8.62TORSIONAL
12H1868X-RAY DIFFRACTION8.62TORSIONAL
21M3564X-RAY DIFFRACTION8.62TORSIONAL
22C3564X-RAY DIFFRACTION8.62TORSIONAL
31B1926X-RAY DIFFRACTION8.62TORSIONAL
32L1926X-RAY DIFFRACTION8.62TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3-3.33750.38031790.34593117329699
3.3375-3.37680.36621650.351831053270100
3.3768-3.4180.3881630.33731103273100
3.418-3.46120.32871450.320831763321100
3.4612-3.50680.34021760.315130903266100
3.5068-3.55480.33381780.307431483326100
3.5548-3.60560.32981530.300631553308100
3.6056-3.65940.32671530.286331853338100
3.6594-3.71660.29161670.268831103277100
3.7166-3.77760.30411700.268131253295100
3.7776-3.84270.28851810.253931053286100
3.8427-3.91260.23681620.244631623324100
3.9126-3.98790.25051870.241931333320100
3.9879-4.06930.23551670.23931613328100
4.0693-4.15780.25891230.221931473270100
4.1578-4.25450.21751800.211931613341100
4.2545-4.36090.23261300.215531573287100
4.3609-4.47880.2151350.204331613296100
4.4788-4.61060.17691650.189431443309100
4.6106-4.75940.18371730.186231263299100
4.7594-4.92950.20512070.179930993306100
4.9295-5.12690.20531610.18831583319100
5.1269-5.36030.24621590.20131383297100
5.3603-5.64290.23581680.220131423310100
5.6429-5.99640.27321480.234331603308100
5.9964-6.45940.26771570.236231653322100
6.4594-7.10950.26841680.232231573325100
7.1095-8.13820.2251610.22331423303100
8.1382-10.2530.19911580.18823146330499
10.253-158.710.30121800.32423140332099
Refinement TLS params.Method: refined / Origin x: 209.23 Å / Origin y: -31.859 Å / Origin z: -14.2974 Å
111213212223313233
T0.485 Å2-0.0549 Å20.0162 Å2-0.6021 Å2-0.0009 Å2--0.5989 Å2
L0.8136 °20.0977 °20.0251 °2-0.5956 °20.24 °2--0.9584 °2
S0.0343 Å °0.1401 Å °-0.2321 Å °0.0803 Å °-0.0462 Å °-0.0358 Å °0.164 Å °0.0472 Å °0.0355 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 224
2X-RAY DIFFRACTION1allB1 - 213
3X-RAY DIFFRACTION1allM15 - 451
4X-RAY DIFFRACTION1allH1 - 224
5X-RAY DIFFRACTION1allC16 - 448
6X-RAY DIFFRACTION1allL1 - 213
7X-RAY DIFFRACTION1allM501
8X-RAY DIFFRACTION1allM502

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