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- PDB-8qb4: Crystal structure of apo-GltTk obtained with in meso crystallizat... -

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Basic information

Entry
Database: PDB / ID: 8qb4
TitleCrystal structure of apo-GltTk obtained with in meso crystallization (H32 space group)
ComponentsProton/glutamate symporter, SDF family
KeywordsMEMBRANE PROTEIN / glutamate transporter / in meso crystallization / aspartate / glutamate
Function / homology
Function and homology information


carboxylic acid transport / symporter activity / membrane / 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
OLEIC ACID / Proton/glutamate symporter, SDF family
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMarin, E. / Guskov, A. / Borshchevskiy, V. / Kovalev, K.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)OCENW.KLEIN.141 Netherlands
CitationJournal: To Be Published
Title: Crystal structure of apo-GltTk obtained with in meso crystallization (H32 space group)
Authors: Marin, E. / Guskov, A. / Borshchevskiy, V. / Kovalev, K.
History
DepositionAug 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2757
Polymers45,5801
Non-polymers1,6956
Water00
1
A: Proton/glutamate symporter, SDF family
hetero molecules

A: Proton/glutamate symporter, SDF family
hetero molecules

A: Proton/glutamate symporter, SDF family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,82521
Polymers136,7413
Non-polymers5,08418
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15170 Å2
ΔGint7 kcal/mol
Surface area46220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.850, 92.850, 335.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Proton/glutamate symporter, SDF family


Mass: 45580.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK0986 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JID0
#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H34O2
Has ligand of interestN

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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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5 / Details: 1.6 M ammonium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97242 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 15646 / % possible obs: 99.2 % / Redundancy: 19.3 % / Biso Wilson estimate: 70.2 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.34 / Net I/σ(I): 8.28
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 0.69 / Num. unique obs: 1538 / CC1/2: 0.201 / Rrim(I) all: 4.649 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.88 Å / SU ML: 0.4751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9032
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2976 783 5.01 %
Rwork0.2536 14861 -
obs0.2558 15644 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.05 Å2
Refinement stepCycle: LAST / Resolution: 2.7→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 75 0 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113155
X-RAY DIFFRACTIONf_angle_d1.39534276
X-RAY DIFFRACTIONf_chiral_restr0.0735530
X-RAY DIFFRACTIONf_plane_restr0.0131523
X-RAY DIFFRACTIONf_dihedral_angle_d14.13971123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.34781290.32532452X-RAY DIFFRACTION99.96
2.87-3.090.3591290.31972449X-RAY DIFFRACTION100
3.09-3.40.3291300.27122460X-RAY DIFFRACTION100
3.4-3.890.30621250.28892377X-RAY DIFFRACTION95.21
3.89-4.90.27611310.22532498X-RAY DIFFRACTION99.7
4.9-42.880.28231390.23122625X-RAY DIFFRACTION100
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)
11.583024619770.377852510752-1.33074187061.17582977522-0.870777203242.19086823813-0.0142681013738-0.194357977529-0.243711005608-0.063135800884-0.1532599131320.0729752333642-0.1857582540330.2386038882360.156337147560.607432913474-0.0944268057424-0.08235822091060.541384675566-0.08353988461650.6436743774112.62636472523.84743518429.5243239024
23.00439707572.321798222-2.431633398382.4487783343-2.326726512772.04617086447-0.1546372722530.556114311919-0.206357396129-0.336972098276-0.0911923817232-0.2296366356480.173789299981-0.3440268720460.1637328098190.647425302130.07963171416780.03508830647610.694538025854-0.1183256311830.868501110115-3.9250963905319.286802079318.4677583815
33.786111973240.483026045188-0.8945257339512.9739356767-1.13764468712.931066190350.0788567661272-0.264706327227-0.2277038129480.188206396913-0.103100996760.263259959052-0.234308007994-0.0992919955525-0.08054315036990.4125725303080.0429628930957-0.03773702432310.313025384932-0.1013358970780.5598339653164.9556123926312.750949835339.745856655
41.66911040967-0.24250941109-0.5520844248961.77301858918-1.350122655633.874277883120.01716061115860.139238059324-0.0256083716728-0.002841091372370.00682235726314-0.0217758103349-0.309798754042-0.0571997009398-0.00910170564370.5519276793990.004885009143190.01026334811090.478005879447-0.02463892111510.6313810536829.5181476151730.513126690329.8718472808
58.98692268750.240690860663-1.784885196471.646819595582.134663748048.856089715840.1555830848130.5890594153140.691498767977-1.18254902154-0.508852916684-0.470058395306-0.862736260715-1.199780271940.6321143701370.7826912845140.1763557792110.1009081767620.4822829729260.0680967595010.508615523962-1.6731577009136.426353389510.5849224326
66.17496495195-0.280660511945-1.40103235593.602970016741.910476384593.139215467160.1888574270960.272887153572-0.9771132458180.394724664079-0.2612741187170.01963433267560.423337335789-0.179546053520.02883383208110.7578269254930.01633009140280.09661997065850.6497507888110.1150003152670.8746278759185.6527039158525.53312529357.4506062388
71.731804527-0.555329277749-0.7527404985010.888394211055-0.3373865545623.59586265319-0.2476523861880.128406227317-0.07590318026890.00800763799418-0.113760733237-0.103737478880.135172863687-0.1998548418420.2559089618890.7273354669060.0315546335992-0.01247397700580.5541542196190.04463384891090.9255982136867.5037549342630.056404275637.2877504485
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 109 )13 - 1091 - 97
22chain 'A' and (resid 110 through 152 )110 - 15298 - 134
33chain 'A' and (resid 153 through 225 )153 - 225135 - 207
44chain 'A' and (resid 226 through 331 )226 - 331208 - 313
55chain 'A' and (resid 332 through 352 )332 - 352314 - 334
66chain 'A' and (resid 353 through 393 )353 - 393335 - 375
77chain 'A' and (resid 394 through 430 )394 - 430376 - 412

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