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- PDB-3kbc: Crystal structure of GltPh K55C-A364C mutant crosslinked with div... -

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Basic information

Entry
Database: PDB / ID: 3kbc
TitleCrystal structure of GltPh K55C-A364C mutant crosslinked with divalent mercury
Components425aa long hypothetical proton glutamate symport protein
KeywordsTRANSPORT PROTEIN / AMINO ACID TRANSPORTER / TRANSMEMBRANE TRANSPORTER / ASPARTATE TRANSPORTER / CYSTEINE CROSS-LINK / INWARD-FACING
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: 3.51 Å
AuthorsReyes, N. / Ginter, C. / Boudker, O.
CitationJournal: Nature / Year: 2009
Title: Transport mechanism of a bacterial homologue of glutamate transporters.
Authors: Reyes, N. / Ginter, C. / Boudker, O.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 13, 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 1.3Sep 6, 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.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_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)135,80715
Polymers134,6683
Non-polymers1,13912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-60.2 kcal/mol
Surface area48120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.142, 206.780, 205.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: HG / End label comp-ID: HG / Refine code: 1 / Auth seq-ID: 6 - 501 / Label seq-ID: 6

Dom-IDAuth asym-IDLabel asym-ID
1AA - E
2BB - I
3CC - M
DetailsBiological unit is the same as asymmetric unit

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Components

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


Mass: 44889.191 Da / Num. of mol.: 3
Mutation: D37H, K40H, K55C, K125H, K132H, K223H, K264H, C321A, A364C, E368H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1295 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O59010
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#4: 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG MME 350, CaCl2, MES, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2008
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 30570 / Num. obs: 29928 / % possible obs: 97.9 % / Redundancy: 8.3 % / Biso Wilson estimate: 109.7 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 6.1
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 6.4 % / Num. unique all: 2776 / % possible all: 92.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NWX

2nwx


Resolution: 3.51→12 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 86.374 / SU ML: 0.548 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1473 5.1 %RANDOM
Rwork0.267 ---
obs0.267 28969 97.22 %-
all-29864 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 110.55 Å2 / Biso mean: 100.882 Å2 / Biso min: 85.38 Å2
Baniso -1Baniso -2Baniso -3
1-5.25 Å20 Å20 Å2
2--2.99 Å20 Å2
3----8.24 Å2
Refinement stepCycle: LAST / Resolution: 3.51→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9060 0 36 0 9096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229258
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.98412636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.09751230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg0.88124.111270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.752151482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.5491518
X-RAY DIFFRACTIONr_chiral_restr0.0810.21602
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216636
X-RAY DIFFRACTIONr_mcbond_it0.1181.56108
X-RAY DIFFRACTIONr_mcangle_it0.22629840
X-RAY DIFFRACTIONr_scbond_it0.28233150
X-RAY DIFFRACTIONr_scangle_it0.5144.52796
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3032 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ATIGHT POSITIONAL0.010.01
BTIGHT POSITIONAL0.010.01
CTIGHT POSITIONAL0.010.01
ATIGHT THERMAL0.120.5
BTIGHT THERMAL0.120.5
CTIGHT THERMAL0.120.5
LS refinement shellResolution: 3.51→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 101 -
Rwork0.41 1634 -
all-1735 -
obs--84.47 %
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)
17.194-3.7947-1.18234.5609-0.47615.66430.3241-0.38610.32060.02110.0529-0.03860.2252-0.4356-0.3770.2026-0.12630.06240.15910.04460.1431-65.5333-22.9995-23.4452
24.2454-1.0481-0.75274.8097-1.809910.54730.1618-0.5181-0.57740.26240.02220.40750.7165-0.841-0.18390.1923-0.21870.00330.35750.16910.294-75.5739-33.4682-14.4507
34.2251-0.1125-2.37872.16590.738410.83780.6749-0.74680.94890.25070.0906-0.0383-2.35631.4908-0.76551.534-0.88950.58660.5755-0.44240.5167-41.50096.6015-25.4452
45.0881.82522.33282.8645-0.02787.7325-0.0382-0.7657-0.8043-0.1039-0.2227-0.53521.15392.24240.26090.71050.91690.05271.58870.2690.5785-25.6637-44.5271-30.6989
58.68662.3288-4.62451.8665-0.72925.84720.3882-0.69390.129-0.12320.0103-0.1983-1.43011.6833-0.39840.4955-0.55240.2010.6289-0.23240.2025-40.5698-9.3169-31.535
62.9481.9118-0.68687.69850.48875.2140.0017-0.6975-0.4828-0.1539-0.25560.23171.42171.79220.25390.43480.46890.04430.7280.17460.3453-41.7484-38.8408-31.2537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 71
2X-RAY DIFFRACTION1A117 - 214
3X-RAY DIFFRACTION2A72 - 116
4X-RAY DIFFRACTION2A215 - 416
5X-RAY DIFFRACTION3B72 - 116
6X-RAY DIFFRACTION3B215 - 416
7X-RAY DIFFRACTION4C72 - 116
8X-RAY DIFFRACTION4C215 - 416
9X-RAY DIFFRACTION5B6 - 71
10X-RAY DIFFRACTION5B117 - 214
11X-RAY DIFFRACTION6C6 - 71
12X-RAY DIFFRACTION6C117 - 214

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