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- PDB-2nwl: Crystal structure of GltPh in complex with L-Asp -

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Basic information

Entry
Database: PDB / ID: 2nwl
TitleCrystal structure of GltPh in complex with L-Asp
Componentsglutamate symport protein
KeywordsTRANSPORT PROTEIN / alpha helical / membrane protein / helical hairpin / unwound region
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: 2.96 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 15, 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: Advisory / 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: glutamate symport protein
B: glutamate symport protein
C: glutamate symport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0509
Polymers133,8813
Non-polymers1,1696
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-69 kcal/mol
Surface area45190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.296, 115.296, 323.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B C
12A B C
13A B C
14A B C

NCS domain segments:

Dom-ID: 1 / Refine code: 1

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRGLUGLUAA10 - 41610 - 416
21TYRTYRGLUGLUBB10 - 41610 - 416
31TYRTYRGLUGLUCC10 - 41610 - 416
12ASPASPASPASPCF501
22ASPASPASPASPCG601
32ASPASPASPASPCH701
13PLMPLMPLMPLMAD801
23PLMPLMPLMPLMBE901
33PLMPLMPLMPLMCI1001
14HOHHOHHOHHOHAJ1101
24HOHHOHHOHHOHBK1201
34HOHHOHHOHHOHCL1301

NCS ensembles :
ID
1
2
3
4
DetailsProtein is a trimer as seen in the asymmetric unit

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Components

#1: Protein glutamate symport protein / GLTPH


Mass: 44626.973 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-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Water ChemComp-HOH / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.48 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.96→100 Å / Num. obs: 15137 / % possible obs: 89.9 % / Redundancy: 5.2 % / Rsym value: 0.074 / Net I/σ(I): 17.1
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.36 / % possible all: 47.8

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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: 2.96→100 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 51.372 / SU ML: 0.396 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1728 4.9 %RANDOM
Rwork0.236 ---
obs0.238 15137 69.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.432 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å21.93 Å20 Å2
2--3.86 Å20 Å2
3----5.79 Å2
Refinement stepCycle: LAST / Resolution: 2.96→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8575 0 78 3 8656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228815
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.98512037
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56551197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62723.718234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.652151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7571518
X-RAY DIFFRACTIONr_chiral_restr0.1010.21539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026321
X-RAY DIFFRACTIONr_nbd_refined0.2760.35967
X-RAY DIFFRACTIONr_nbtor_refined0.3490.56425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.5635
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.36
X-RAY DIFFRACTIONr_mcbond_it1.09226054
X-RAY DIFFRACTIONr_mcangle_it1.83439484
X-RAY DIFFRACTIONr_scbond_it1.15123062
X-RAY DIFFRACTIONr_scangle_it1.55332553
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2837TIGHT POSITIONAL0.060.05
1B2837TIGHT POSITIONAL0.050.05
1C2837TIGHT POSITIONAL0.050.05
1A2837TIGHT THERMAL2.045
1B2837TIGHT THERMAL1.645
1C2837TIGHT THERMAL1.455
2A9TIGHT POSITIONAL0.030.05
2B9TIGHT POSITIONAL0.060.05
2C9TIGHT POSITIONAL0.040.05
2A9TIGHT THERMAL2.385
2B9TIGHT THERMAL3.115
2C9TIGHT THERMAL1.095
3A17TIGHT POSITIONAL0.070.05
3B17TIGHT POSITIONAL0.090.05
3C17TIGHT POSITIONAL0.040.05
3A17TIGHT THERMAL0.635
3B17TIGHT THERMAL2.165
3C17TIGHT THERMAL2.255
4A1TIGHT POSITIONAL0.05
4B1TIGHT POSITIONAL0.05
4C1TIGHT POSITIONAL0.05
4A1TIGHT THERMAL6.445
4B1TIGHT THERMAL8.875
4C1TIGHT THERMAL2.425
LS refinement shellResolution: 2.956→3.033 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 12 -
Rwork0.366 316 -
obs-328 8.76 %
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)
10.71880.58410.42821.98070.40992.402-0.2050.10830.13790.13910.277-0.01090.21280.1715-0.0720.15570.08710.02940.22470.0333-0.068612.05464.190713.663
21.152-0.5405-0.11461.5177-0.6832.16580.0650.22110.3344-0.30550.08410.2338-0.6749-0.1496-0.14910.64380.0841-0.03760.29460.12830.32314.288345.440.1171
31.2958-0.2072-0.54791.46560.27991.5917-0.02460.01440.1746-0.1130.1595-0.4448-0.4850.6094-0.13480.2395-0.2939-0.07530.702-0.08350.372845.69630.11862.1073
485.797-4.6945-1.992225.74715.977147.3141-0.5551-0.69750.15970.58780.7178-0.65630.52662.4069-0.1627-0.0134-0.00380.0147-0.0052-0.0056-0.007825.50724.11049.4729
514.7316-6.2487-34.4924131.431160.407497.0321-0.7922-3.2011-1.3274-1.5039-2.13194.49941.78542.28152.9241-0.0096-0.022-0.0139-0.0581-0.0043-0.021-0.138332.06990.8638
6130.949379.4837-65.2675111.0212-78.3331120.86831.15133.4020.9457-1.8057-0.1297-0.6193-1.9062.0445-1.02160.0052-0.00440.00350.0025-0.00770.003636.859339.1181-4.4406
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA10 - 41610 - 416
21AH1101
31CD501
42BB10 - 41610 - 416
52BI1201
62CD601
73CC10 - 41610 - 416
83CJ1301
93CD701
104AE801
115BF901
126CG1001

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