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- PDB-4gx0: Crystal structure of the GsuK L97D mutant -

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Basic information

Entry
Database: PDB / ID: 4gx0
TitleCrystal structure of the GsuK L97D mutant
ComponentsTrkA domain protein
KeywordsTRANSPORT PROTEIN / Membrane Protein / Ion Channel / ADP Binding / NAD Binding / Membrane
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / nucleotide binding / membrane / metal ion binding
Similarity search - Function
Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain ...Regulator of K+ conductance, C-terminal domain / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Helix Hairpins - #70 / Potassium channel domain / Ion channel / Helix Hairpins / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / alpha-D-glucopyranose / : / PHOSPHATE ION / TrkA domain protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.601 Å
AuthorsKong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
CitationJournal: elife / Year: 2012
Title: Distinct gating mechanisms revealed by the structures of a multi-ligand gated K(+) channel.
Authors: Kong, C. / Zeng, W. / Ye, S. / Chen, L. / Sauer, D.B. / Lam, Y. / Derebe, M.G. / Jiang, Y.
History
DepositionSep 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _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 / _pdbx_struct_special_symmetry.label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TrkA domain protein
B: TrkA domain protein
C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,57833
Polymers247,3294
Non-polymers2,24929
Water7,044391
1
A: TrkA domain protein
B: TrkA domain protein
hetero molecules

A: TrkA domain protein
B: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,19536
Polymers247,3294
Non-polymers2,86632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13350 Å2
ΔGint-109 kcal/mol
Surface area81230 Å2
MethodPISA
2
C: TrkA domain protein
D: TrkA domain protein
hetero molecules

C: TrkA domain protein
D: TrkA domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,96030
Polymers247,3294
Non-polymers1,63126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area12960 Å2
ΔGint-110 kcal/mol
Surface area81870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.934, 111.670, 164.133
Angle α, β, γ (deg.)90.00, 134.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-601-

K

21A-602-

K

31A-603-

K

41A-604-

K

51A-605-

K

61B-603-

K

71C-601-

K

81C-602-

K

91C-603-

K

101C-604-

K

111C-608-

K

121D-601-

K

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TrkA domain protein


Mass: 61832.238 Da / Num. of mol.: 4 / Mutation: E52A, Q77E, L97D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU0527 / Plasmid: pQE-70 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q74FS9

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 416 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 13-18% PEG 3350, 250-500mM KSCN, 100mM CHES, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 87305 / % possible obs: 94.7 % / Observed criterion σ(I): 1.1839
Reflection shellResolution: 2.6→2.64 Å / % possible all: 57.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.601→30.937 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 4371 5.01 %
Rwork0.2026 --
obs0.205 87242 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.367 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5609 Å20 Å21.4096 Å2
2---5.1297 Å20 Å2
3---2.5688 Å2
Refinement stepCycle: LAST / Resolution: 2.601→30.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14235 0 104 391 14730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414601
X-RAY DIFFRACTIONf_angle_d0.66619890
X-RAY DIFFRACTIONf_dihedral_angle_d13.5895290
X-RAY DIFFRACTIONf_chiral_restr0.0482385
X-RAY DIFFRACTIONf_plane_restr0.0032529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6009-2.63050.3805810.30041560X-RAY DIFFRACTION54
2.6305-2.66140.3221000.27211888X-RAY DIFFRACTION65
2.6614-2.69380.30461120.27762094X-RAY DIFFRACTION72
2.6938-2.72790.31471320.2692329X-RAY DIFFRACTION81
2.7279-2.76380.3461230.27162568X-RAY DIFFRACTION88
2.7638-2.80160.31241360.25992737X-RAY DIFFRACTION93
2.8016-2.84160.3141510.25842715X-RAY DIFFRACTION96
2.8416-2.8840.30281420.24962910X-RAY DIFFRACTION97
2.884-2.92910.28411530.24792827X-RAY DIFFRACTION99
2.9291-2.9770.30881580.2432855X-RAY DIFFRACTION99
2.977-3.02830.33041560.23812930X-RAY DIFFRACTION100
3.0283-3.08330.28541510.2312930X-RAY DIFFRACTION100
3.0833-3.14260.26971530.22192894X-RAY DIFFRACTION100
3.1426-3.20670.30191500.22442901X-RAY DIFFRACTION100
3.2067-3.27630.26531260.21062952X-RAY DIFFRACTION100
3.2763-3.35250.26281640.19992891X-RAY DIFFRACTION100
3.3525-3.43620.23891460.19062895X-RAY DIFFRACTION100
3.4362-3.5290.21661450.1822938X-RAY DIFFRACTION100
3.529-3.63270.23351480.17732924X-RAY DIFFRACTION100
3.6327-3.74970.25381640.17892893X-RAY DIFFRACTION100
3.7497-3.88350.22341570.17612920X-RAY DIFFRACTION100
3.8835-4.03870.22531640.17022922X-RAY DIFFRACTION100
4.0387-4.2220.20941340.16612919X-RAY DIFFRACTION100
4.222-4.4440.19811500.15612947X-RAY DIFFRACTION100
4.444-4.72150.20111310.15192916X-RAY DIFFRACTION100
4.7215-5.08460.20271720.1582900X-RAY DIFFRACTION100
5.0846-5.59360.21891800.17072921X-RAY DIFFRACTION100
5.5936-6.39680.24011670.19182917X-RAY DIFFRACTION100
6.3968-8.03580.25161560.20052953X-RAY DIFFRACTION100
8.0358-30.93920.2251690.21382925X-RAY DIFFRACTION97
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)
11.4026-0.2634-0.28990.463-0.05880.8386-0.02420.03250.2250.04010.0387-0.2808-0.0580.1478-0.0020.4169-0.0755-0.01960.23150.00370.3756-48.1593-49.659461.1642
20.9989-0.1889-0.36670.49220.15741.91670.01890.05340.21920.0959-0.0017-0.2576-0.21870.0836-0.00430.3345-0.04220.03150.22830.0110.4957-105.6045-21.5465119.0991
30.7620.0977-0.52080.9416-0.83273.0932-0.13690.0515-0.0015-0.0640.0984-0.02530.14660.10770.03820.07320.0418-0.04260.16630.0120.1472-31.497312.05460.43
44.2786-0.56431.12110.9753-0.18810.96150.0393-0.0315-0.2849-0.04490.01010.03140.0686-0.0431-0.05150.1545-0.10910.0490.1142-0.04260.0689-55.127611.645133.7217
51.25680.2042-1.03290.489-0.12853.58070.0250.1144-0.2372-0.1059-0.0685-0.14340.3486-0.10540.04850.18910.0508-0.040.1586-0.12160.2783-89.48739.9732117.8791
63.9134-1.4250.2261.54380.20910.9836-0.01390.0256-0.1583-0.15660.08350.09220.0688-0.0973-0.0080.16830.03260.02970.1435-0.01540.1023-114.404739.973791.2744
70.80370.0499-0.6912.54030.72671.79470.13910.1766-0.0678-0.5276-0.0489-0.5847-0.04260.0382-0.08470.4821-0.07110.04820.5094-0.03740.4431-52.340412.63874.5082
81.7716-1.21190.22922.7198-0.55952.83960.0636-0.06060.54150.2134-0.0608-0.68040.04620.7109-0.14910.22520.0196-0.03530.4516-0.22580.4202-59.955342.5574118.4813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 18:118 ) OR ( CHAIN B AND RESID 18:118 )A18 - 118
2X-RAY DIFFRACTION1( CHAIN A AND RESID 18:118 ) OR ( CHAIN B AND RESID 18:118 )B18 - 118
3X-RAY DIFFRACTION2( CHAIN C AND RESID 19:118 ) OR ( CHAIN D AND RESID 18:118 )C19 - 118
4X-RAY DIFFRACTION2( CHAIN C AND RESID 19:118 ) OR ( CHAIN D AND RESID 18:118 )D18 - 118
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 ) )A119 - 261
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 ) )A350 - 480
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:480 OR RESID 606:606 ) )A606
8X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 601:601 ) )B119 - 260
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 601:601 ) )B350 - 480
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 601:601 ) )B601
11X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 605:605 ) )C119 - 261
12X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 605:605 ) )C351 - 482
13X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 605:605 ) )C605
14X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 ) )D119 - 261
15X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 ) )D351 - 482
16X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 602:602 ) )D602
17X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B261 - 349
18X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B481 - 564
19X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C262 - 350
20X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C483 - 564

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