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- PDB-4x2s: Crystal structure of 276S/M395R-GltPh in inward-facing conformation -

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Basic information

Entry
Database: PDB / ID: 4x2s
TitleCrystal structure of 276S/M395R-GltPh in inward-facing conformation
Components425aa long hypothetical proton glutamate symport protein
KeywordsTRANSPORT PROTEIN / Amino Acid Secondary Transporters / Sodium Coupled Aspartate Transporter
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
Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
ASPARTIC ACID / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.21 Å
AuthorsAkyuz, N. / Boudker, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5U54GM087519 United States
CitationJournal: Nature / Year: 2015
Title: Transport domain unlocking sets the uptake rate of an aspartate transporter.
Authors: Akyuz, N. / Georgieva, E.R. / Zhou, Z. / Stolzenberg, S. / Cuendet, M.A. / Khelashvili, G. / Altman, R.B. / Terry, D.S. / Freed, J.H. / Weinstein, H. / Boudker, O. / Blanchard, S.C.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)134,23512
Polymers133,6973
Non-polymers5379
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-103 kcal/mol
Surface area52900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.651, 121.651, 578.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22B
32C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A60 - 74
2111B60 - 74
3111C60 - 74
1211A130 - 206
2211B130 - 206
3211C130 - 206
1121A85 - 119
2121B85 - 119
3121C85 - 119
1221A228 - 500
2221B228 - 500
3221C228 - 500
1131B1 - 500
2131C1 - 500

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.513566, -0.851047, -0.109405), (0.831332, -0.461943, -0.309023), (0.212454, -0.249656, 0.944741)21.63562, -119.665939, -23.665079
3given(-0.501734, 0.844017, 0.189467), (-0.858701, -0.459544, -0.226831), (-0.104381, -0.276505, 0.955327)115.207642, -41.713299, -10.67126
4given(1), (1), (1)
5given(-0.546904, -0.832925, -0.084452), (0.836633, -0.540053, -0.09159), (0.030679, -0.120746, 0.992209)24.54216, -116.005447, -7.1753
6given(-0.465741, 0.859652, 0.209962), (-0.87897, -0.476869, 0.00271), (0.102455, -0.183288, 0.977706)114.790619, -33.52956, -14.02355
7given(1), (1), (1)
8given(-0.477709, -0.874645, -0.082399), (0.850022, -0.436481, -0.294867), (0.221939, -0.210902, 0.951979)19.46089, -118.883003, -22.02067

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Components

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


Mass: 44565.766 Da / Num. of mol.: 3
Mutation: R276S, M395R, D37H, K40H, K125H, K132H, K223H, K264H, E368H, C321A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: Escherichia coli (E. coli) / References: UniProt: O59010
#2: 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
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.62 Å3/Da / Density % sol: 73.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 mM sodium acetate, pH 5.6-6, 18-20 % PEG 400, 100-150 mM magnesium acetate
PH range: 5.6-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 15575 / % possible obs: 82 % / Redundancy: 10.8 % / Net I/σ(I): 23

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Processing

SoftwareName: REFMAC / Version: 5.8.0069 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWX

2nwx


Resolution: 4.21→20 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.858 / SU B: 171.825 / SU ML: 0.958 / Cross valid method: THROUGHOUT / ESU R Free: 1.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31363 824 5.1 %RANDOM
Rwork0.27795 ---
obs0.27964 15417 83.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 197.282 Å2
Baniso -1Baniso -2Baniso -3
1--3.44 Å2-1.72 Å20 Å2
2---3.44 Å20 Å2
3---11.15 Å2
Refinement stepCycle: LAST / Resolution: 4.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9064 0 33 0 9097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199262
X-RAY DIFFRACTIONr_bond_other_d0.0020.029452
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.98412640
X-RAY DIFFRACTIONr_angle_other_deg0.865321612
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0470.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021941
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7958.6364930
X-RAY DIFFRACTIONr_mcbond_other3.7968.6374929
X-RAY DIFFRACTIONr_mcangle_it6.54412.9486152
X-RAY DIFFRACTIONr_mcangle_other6.54312.9476153
X-RAY DIFFRACTIONr_scbond_it3.4818.9964332
X-RAY DIFFRACTIONr_scbond_other3.48194329
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.13413.3356487
X-RAY DIFFRACTIONr_long_range_B_refined10.32485.237962
X-RAY DIFFRACTIONr_long_range_B_other10.32485.2247963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A137422.08
12B137417.55
13C137421.68
21A330619.38
22B330613.84
23C330626.31
31B620617.11
LS refinement shellResolution: 4.21→4.314 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.46 9 -
Rwork0.365 234 -
obs--18.26 %
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)
14.4415-1.06960.01365.87430.76131.7508-0.82350.0588-0.17121.25650.2493-1.14190.31490.29110.57410.87510.1263-0.20761.18010.24750.635371.774-48.651-24.826
21.76310.56330.35854.13260.09691.1370.00960.3438-0.62780.67280.17560.88430.3113-0.2363-0.18521.4899-0.18910.90091.29020.17121.039234.296-74.512-23.742
35.0743-0.4649-1.22262.4061-0.01432.6943-0.8469-0.17240.8090.70110.39940.9388-0.3295-0.72020.44751.15230.23970.18571.2698-0.03940.820330-29.194-19.689
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C6 - 420
2X-RAY DIFFRACTION2A12 - 416
3X-RAY DIFFRACTION3B6 - 416

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