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- PDB-3v8f: Crystal structure of crosslinked GltPh V216C-M385C mutant -

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Basic information

Entry
Database: PDB / ID: 3v8f
TitleCrystal structure of crosslinked GltPh V216C-M385C mutant
Componentssodium-coupled L-aspartate transporter
KeywordsTRANSPORT PROTEIN / sodium ions / L-arpartate / membrane
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 / : / Glutamate transporter homolog
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsVerdon, G. / Boudker, O.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Crystal structure of an asymmetric trimer of a bacterial glutamate transporter homolog.
Authors: Verdon, G. / Boudker, O.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sodium-coupled L-aspartate transporter
B: sodium-coupled L-aspartate transporter
C: sodium-coupled L-aspartate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,89715
Polymers133,7583
Non-polymers1,13912
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-160 kcal/mol
Surface area47900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.300, 199.810, 111.251
Angle α, β, γ (deg.)90.00, 117.08, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 426
2111B6 - 426
3111C6 - 426

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Components

#1: Protein sodium-coupled L-aspartate transporter / hypothetical proton glutamate symport protein


Mass: 44585.840 Da / Num. of mol.: 3
Mutation: D37H, K40H, K125H, K132H, V216C, K223H, K264H, C321A, E368H, M385C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (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
#4: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg

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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: 4.6 Å3/Da / Density % sol: 73.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15 - 20% PEG 350 MME, 0.1 M Hepes, ph = 7.4, 0.15 - 0.3 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.8→96.7 Å / Num. all: 47156 / Num. obs: 46875 / % possible obs: 99.4 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→30 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.921 / SU B: 79.591 / SU ML: 0.502 / Cross valid method: THROUGHOUT / ESU R Free: 0.629 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25457 1217 5.1 %RANDOM
Rwork0.24339 ---
obs0.244 22480 99.55 %-
all-23786 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 247.219 Å2
Baniso -1Baniso -2Baniso -3
1-4.48 Å20 Å2-1.46 Å2
2--6.84 Å20 Å2
3----12.65 Å2
Refinement stepCycle: LAST / Resolution: 3.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9119 0 36 0 9155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229323
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.98212718
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.30851228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63323.789285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.43151500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4951524
X-RAY DIFFRACTIONr_chiral_restr0.1040.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216712
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4181.56098
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87229832
X-RAY DIFFRACTIONr_scbond_it1.54433225
X-RAY DIFFRACTIONr_scangle_it3.0154.52886
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3050 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.040.05
Btight positional0.040.05
Ctight positional0.050.05
Atight thermal0.060.5
Btight thermal0.060.5
Ctight thermal0.070.5
LS refinement shellResolution: 3.799→3.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 81 -
Rwork0.375 1617 -
obs--97.64 %
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)
122.0413-1.2514-0.90544.6246-0.72527.38340.4018-2.2721.06190.8466-0.2266-0.3794-2.99832.0666-0.17511.6446-0.7024-0.0221.0009-0.39650.4367.28256.16827.06
28.4805-2.04280.59054.7315-0.68957.86950.4577-1.20892.42490.58480.4022-0.323-2.99940.4534-0.85993.4157-0.88710.39310.8646-0.83461.64886.272272.546630.1764
39.28494.2816-0.835512.21742.38479.2739-0.6014-1.4257-1.13040.21830.03170.5611.06560.67220.56970.21720.2150.09080.45650.29940.3599-2.650527.510424.6386
410.25331.3849-1.17877.2416-1.217214.9305-0.0048-1.6987-1.0760.74410.3264-0.54411.30331.8053-0.32150.6320.65540.00231.08380.42790.691110.631919.539830.9995
58.9409-4.43061.633712.4764-0.98896.4555-0.0857-0.81031.13510.1454-0.14330.3635-2.027-2.15160.22910.75880.65260.11930.7852-0.14140.4462-21.829150.651120.0327
69.859-0.0298-3.40127.5911.507811.94960.222-0.23650.0742-0.0806-0.22690.7273-0.4802-2.45120.0050.17670.4691-0.07591.70120.04290.3801-36.174542.12319.8267
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 74
2X-RAY DIFFRACTION1A131 - 220
3X-RAY DIFFRACTION2A75 - 130
4X-RAY DIFFRACTION2A221 - 420
5X-RAY DIFFRACTION3B6 - 74
6X-RAY DIFFRACTION3B131 - 220
7X-RAY DIFFRACTION4B75 - 130
8X-RAY DIFFRACTION4B221 - 420
9X-RAY DIFFRACTION5C6 - 74
10X-RAY DIFFRACTION5C131 - 220
11X-RAY DIFFRACTION6C75 - 130
12X-RAY DIFFRACTION6C221 - 420

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