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- PDB-2nwx: Crystal structure of GltPh in complex with L-aspartate and sodium ions -

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Basic information

Entry
Database: PDB / ID: 2nwx
TitleCrystal structure of GltPh in complex with L-aspartate and sodium ions
Components425aa long hypothetical proton glutamate symport protein
KeywordsTRANSPORT PROTEIN / amino acid transporter / transmembrane transporter / aspartate transporter / binding site / sodium binding / substrate binding
Function / homology
Function and homology information


amino acid:sodium symporter activity / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / chloride transmembrane transporter activity / protein homotrimerization / chloride transmembrane transport / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Proton glutamate symport protein / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ASPARTIC ACID / PALMITIC ACID / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsGouaux, E. / Boudker, O. / Ryan, R. / Yernool, D. / Shimamoto, K.
CitationJournal: Nature / Year: 2007
Title: Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter.
Authors: Boudker, O. / Ryan, R.M. / Yernool, D. / Shimamoto, K. / Gouaux, E.
History
DepositionNov 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 425aa long hypothetical proton glutamate symport protein
B: 425aa long hypothetical proton glutamate symport protein
C: 425aa long hypothetical proton glutamate symport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,23215
Polymers133,9263
Non-polymers1,30712
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-97 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.473, 115.473, 324.227
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
11A
21B
31C
12A
22A
32A
13A
23B
33C
14A
24B
34C

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLUAA12 - 41612 - 416
21VALVALGLUGLUBB12 - 41612 - 416
31VALVALGLUGLUCC12 - 41612 - 416
12ASPASPASPASPAF425
22ASPASPASPASPAG426
32ASPASPASPASPAH427
13PLMPLMPLMPLMAI428
23PLMPLMPLMPLMBL425
33PLMPLMPLMPLMCO425
14NANAHOHHOHAD - P423 - 429
24NANAHOHHOHBJ - Q423 - 426
34NANAHOHHOHCM - R423 - 426

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein 425aa long hypothetical proton glutamate symport protein


Mass: 44641.945 Da / Num. of mol.: 3 / Mutation: D37H, K40H, K125H, K132H, K223H, K264H, E368H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: O59010
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.978 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.29→100 Å / Num. all: 25514 / Num. obs: 25514 / Redundancy: 5.2 % / Rsym value: 9.4 / Net I/σ(I): 17.1
Reflection shellResolution: 3.29→3.72 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 17.7 / Rsym value: 34.8 / % possible all: 30.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1xfh

1xfh


Resolution: 3.29→100 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.878 / SU B: 30.957 / SU ML: 0.514 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.645 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.286 1261 4.9 %RANDOM
Rwork0.263 ---
obs0.265 25514 69.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 134.632 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å21.43 Å20 Å2
2--2.85 Å20 Å2
3----4.28 Å2
Refinement stepCycle: LAST / Resolution: 3.29→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8509 0 84 3 8596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228734
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.98311923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16851191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78323.766231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.508151279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2771518
X-RAY DIFFRACTIONr_chiral_restr0.1020.21527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026261
X-RAY DIFFRACTIONr_nbd_refined0.250.35502
X-RAY DIFFRACTIONr_nbtor_refined0.3320.56309
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.5580
X-RAY DIFFRACTIONr_metal_ion_refined0.3220.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.37
X-RAY DIFFRACTIONr_mcbond_it1.04325929
X-RAY DIFFRACTIONr_mcangle_it1.85539418
X-RAY DIFFRACTIONr_scbond_it0.70722850
X-RAY DIFFRACTIONr_scangle_it1.14232505
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2812TIGHT POSITIONAL0.050.05
12B2812TIGHT POSITIONAL0.050.05
13C2812TIGHT POSITIONAL0.040.05
11A2812TIGHT THERMAL5.835
12B2812TIGHT THERMAL3.335
13C2812TIGHT THERMAL3.255
22A9TIGHT POSITIONAL0.040.05
22A9TIGHT POSITIONAL0.040.05
22B9TIGHT POSITIONAL0.020.05
22A9TIGHT THERMAL7.415
22A9TIGHT THERMAL5.125
22B9TIGHT THERMAL2.345
33B17TIGHT POSITIONAL0.030.05
33C17TIGHT POSITIONAL0.040.05
33C17TIGHT POSITIONAL0.030.05
33B17TIGHT THERMAL1.355
33C17TIGHT THERMAL1.025
33C17TIGHT THERMAL0.795
42B3TIGHT POSITIONAL0.090.05
43C3TIGHT POSITIONAL0.050.05
41A3TIGHT POSITIONAL0.070.05
42B3TIGHT THERMAL9.825
43C3TIGHT THERMAL12.115
41A3TIGHT THERMAL8.585
LS refinement shellResolution: 3.293→3.379 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 20 -
Rwork0.413 309 -
obs-329 12.05 %

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