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- PDB-5cfy: CRYSTAL STRUCTURE OF GLTPH R397A IN COMPLEX WITH NA+ AND L-ASP -

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Basic information

Entry
Database: PDB / ID: 5cfy
TitleCRYSTAL STRUCTURE OF GLTPH R397A IN COMPLEX WITH NA+ AND L-ASP
Components425aa long hypothetical proton glutamate symport protein
KeywordsTRANSPORT PROTEIN / ASPARTATE TRANSPORTER / MEMBRANE PROTEIN
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: 3.5 Å
AuthorsBoudker, O. / Oh, S.
CitationJournal: Elife / Year: 2014
Title: Coupled ion binding and structural transitions along the transport cycle of glutamate transporters.
Authors: Verdon, G. / Oh, S. / Serio, R.N. / Boudker, O.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionApr 20, 2016ID: 4OYG
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ref_seq_dif.details

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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
D: 425aa long hypothetical proton glutamate symport protein
E: 425aa long hypothetical proton glutamate symport protein
F: 425aa long hypothetical proton glutamate symport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,99524
Polymers268,9216
Non-polymers1,07418
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19670 Å2
ΔGint-339 kcal/mol
Surface area89610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.958, 116.958, 313.517
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A6 - 427
2114B6 - 427
3114C6 - 427
4114D6 - 427
5114E6 - 427
6114F6 - 427

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Components

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


Mass: 44820.145 Da / Num. of mol.: 6 / Mutation: D37H, K40H, K132H, K223H, K264H, E368H, R397A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1295 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B / References: UniProt: O59010
#2: Chemical
ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.6 Å3/Da / Density % sol: 73.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG400, SODIUM CHLORIDE, CITRATE/TRIS / PH range: 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.5→15 Å / Num. obs: 55613 / % possible obs: 98.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.6
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 0.4 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NWX

2nwx


Resolution: 3.5→15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 102.928 / SU ML: 0.619 / Cross valid method: THROUGHOUT / ESU R Free: 0.606 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2955 5 %RANDOM
Rwork0.249 ---
obs0.251 55613 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 152.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.35 Å2-2.18 Å20 Å2
2---4.35 Å20 Å2
3---14.12 Å2
Refinement stepCycle: LAST / Resolution: 3.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18168 0 66 6 18240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01918594
X-RAY DIFFRACTIONr_bond_other_d0.0150.0218948
X-RAY DIFFRACTIONr_angle_refined_deg2.0171.98325368
X-RAY DIFFRACTIONr_angle_other_deg2.266343332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78452460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.10623.913552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.919152982
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5481542
X-RAY DIFFRACTIONr_chiral_restr0.1150.23204
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120658
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023900
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_it3.45710.4519876
X-RAY DIFFRACTIONr_mcbond_other3.45710.4519875
X-RAY DIFFRACTIONr_mcangle_it5.59115.6812324
X-RAY DIFFRACTIONr_mcangle_other5.59115.6812325
X-RAY DIFFRACTIONr_scbond_it2.95310.718718
X-RAY DIFFRACTIONr_scbond_other2.95310.7118715
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.14915.96313043
X-RAY DIFFRACTIONr_long_range_B_refined8.69285.26522819
X-RAY DIFFRACTIONr_long_range_B_other8.69185.26622820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 6201 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.180.5
2Bmedium positional0.180.5
3Cmedium positional0.170.5
4Dmedium positional0.170.5
5Emedium positional0.180.5
6Fmedium positional0.180.5
1Amedium thermal5.042
2Bmedium thermal4.042
3Cmedium thermal4.932
4Dmedium thermal4.782
5Emedium thermal5.072
6Fmedium thermal4.072
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 189 -
Rwork0.418 3812 -
obs--93.7 %
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)
11.1512-0.36470.51071.0373-0.54331.0197-0.0074-0.00970.09280.2191-0.04080.42390.1846-0.41730.04810.3974-0.05510.14441.01220.17450.5049-55.241858.320310.1582
21.53820.465-0.5971.5403-0.47181.607-0.0344-0.23580.15380.20270.144-0.038-0.5468-0.0748-0.10960.59730.1336-0.00220.5738-0.09770.0331-19.927385.459115.9887
30.915-0.19320.34171.23810.57872.11780.0011-0.2122-0.4296-0.01310.0190.25490.54850.0398-0.02010.61360.0488-0.04240.48340.12050.2346-13.582241.94626.6002
40.91480.2142-0.3191.24610.61521.9793-0.01660.20870.43040.02950.03560.2415-0.51160.0302-0.0190.6263-0.04920.03960.49120.11460.2301-13.593693.1089-37.532
51.16520.3663-0.47391.103-0.49331.0626-0.02240.0379-0.1001-0.2323-0.02390.4237-0.1786-0.44330.04630.39450.0723-0.13690.99980.18190.4948-55.228276.7465-41.0938
61.4544-0.4210.6561.6083-0.46171.5953-0.01660.2562-0.1454-0.20070.1405-0.05660.5296-0.078-0.12380.6-0.13440.00090.579-0.10250.0365-19.9249.598-46.9227
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 416
2X-RAY DIFFRACTION1A501 - 503
3X-RAY DIFFRACTION2B6 - 416
4X-RAY DIFFRACTION2B501 - 503
5X-RAY DIFFRACTION3C6 - 416
6X-RAY DIFFRACTION3C501 - 503
7X-RAY DIFFRACTION4D6 - 416
8X-RAY DIFFRACTION4D501 - 503
9X-RAY DIFFRACTION5E6 - 416
10X-RAY DIFFRACTION5E501 - 503
11X-RAY DIFFRACTION6F6 - 416
12X-RAY DIFFRACTION6F501 - 503

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