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- PDB-4gx1: Crystal structure of the GsuK bound to ADP -

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Basic information

Entry
Database: PDB / ID: 4gx1
TitleCrystal structure of the GsuK bound to ADP
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
ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / : / PHOSPHATE ION / TrkA domain protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Feb 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)250,80033
Polymers247,3294
Non-polymers3,47129
Water4,918273
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)250,47932
Polymers247,3294
Non-polymers3,15028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13530 Å2
ΔGint-114 kcal/mol
Surface area81620 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)251,12234
Polymers247,3294
Non-polymers3,79330
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area13260 Å2
ΔGint-116 kcal/mol
Surface area81800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.323, 111.442, 164.743
Angle α, β, γ (deg.)90.00, 134.93, 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

41B-601-

K

51B-602-

K

61B-603-

K

71C-601-

K

81C-602-

K

91C-603-

K

101D-601-

K

111D-602-

K

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Components

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Protein / Sugars , 2 types, 8 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
#6: 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.: 4
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 , 6 types, 298 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 60.05 %
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: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 72260 / % possible obs: 96.4 % / Observed criterion σ(I): 0.97777
Reflection shellResolution: 2.8→2.85 Å / % possible all: 88.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→41.47 Å / SU ML: 0.48 / σ(F): 1.34 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 3623 5.06 %Random
Rwork0.2125 ---
obs0.2147 71566 96.73 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.847 Å2 / ksol: 0.267 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.179 Å2-0 Å2-0.003 Å2
2---14.2443 Å20 Å2
3---10.0653 Å2
Refinement stepCycle: LAST / Resolution: 2.8→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14244 0 185 273 14702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514702
X-RAY DIFFRACTIONf_angle_d0.90220046
X-RAY DIFFRACTIONf_dihedral_angle_d16.8175402
X-RAY DIFFRACTIONf_chiral_restr0.0632401
X-RAY DIFFRACTIONf_plane_restr0.0042535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83690.35591300.32772547X-RAY DIFFRACTION96
2.8369-2.87570.38591190.3282695X-RAY DIFFRACTION98
2.8757-2.91680.41531600.31512588X-RAY DIFFRACTION98
2.9168-2.96030.35861320.30482656X-RAY DIFFRACTION98
2.9603-3.00660.31551470.32648X-RAY DIFFRACTION98
3.0066-3.05590.37561540.27362572X-RAY DIFFRACTION98
3.0559-3.10850.31961460.26632677X-RAY DIFFRACTION98
3.1085-3.1650.30971400.26612630X-RAY DIFFRACTION98
3.165-3.22590.31811240.26482643X-RAY DIFFRACTION98
3.2259-3.29170.31891420.24842640X-RAY DIFFRACTION98
3.2917-3.36330.2971440.2352614X-RAY DIFFRACTION98
3.3633-3.44150.28671480.21912613X-RAY DIFFRACTION97
3.4415-3.52750.29481340.21532645X-RAY DIFFRACTION98
3.5275-3.62280.24881220.21372636X-RAY DIFFRACTION98
3.6228-3.72930.2621580.22192595X-RAY DIFFRACTION97
3.7293-3.84960.25321390.19422651X-RAY DIFFRACTION97
3.8496-3.98710.27391420.19062610X-RAY DIFFRACTION97
3.9871-4.14660.20421230.18342636X-RAY DIFFRACTION97
4.1466-4.33510.20271500.16682595X-RAY DIFFRACTION97
4.3351-4.56340.21221400.15352573X-RAY DIFFRACTION96
4.5634-4.84890.1761510.15322625X-RAY DIFFRACTION96
4.8489-5.22270.22551320.16142593X-RAY DIFFRACTION96
5.2227-5.7470.27571240.2162571X-RAY DIFFRACTION95
5.747-6.57580.26281270.23232614X-RAY DIFFRACTION95
6.5758-8.2740.22891470.20132552X-RAY DIFFRACTION94
8.274-41.47430.23621480.22952524X-RAY DIFFRACTION90
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)
12.11580.361-0.42851.5880.30822.0274-0.0238-0.1128-0.19320.41840.133-0.10570.3649-0.0234-0.09220.52280.0424-0.07510.37080.07650.64892.690348.78949.2215
22.0764-0.7832-0.18381.95690.7621.5649-0.0569-0.2071-0.27230.5470.06620.13510.2652-0.064-0.04180.71940.0176-0.02240.36590.06260.4918-56.056420.871967.633
36.95873.0777-1.12672.1159-0.40950.61330.1329-0.09440.09090.17250.0159-0.01160.076-0.0093-0.14020.37230.0276-0.05740.3385-0.05690.2382.0118-12.94725.8048
40.67830.29291.57361.41251.91166.9262-0.0272-0.04440.0526-0.00930.07360.0671-0.3219-0.01010.01180.30.04870.08920.38140.13980.6605-24.7555-12.51942.4619
56.35081.3661-1.2910.8228-0.52870.9049-0.04150.11860.17870.1515-0.02580.0106-0.1608-0.01590.05960.57230.1201-0.07350.3317-0.08580.3505-57.111-40.637983.6597
60.74980.2320.80592.32453.11897.3893-0.0378-0.01250.034-0.02050.01720.1774-0.1171-0.06870.02750.25220.0380.04090.37860.00560.4594-83.8747-40.717559.1903
75.3742-2.4579-1.25167.4271.41645.0477-0.2406-0.50760.08031.35010.10071.0432-0.319-0.61520.11840.67880.04650.09810.80280.15091.0114-54.0499-13.34755.6674
87.20272.21881.94136.3432.91024.7346-0.0079-1.04420.32490.8492-0.0461-0.22980.50340.2371-0.02260.87660.2944-0.0040.7791-0.00350.503-56.2629-43.0763113.2972
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 350:481 OR RESID 604:604 OR RESID 606:606 ) )A119 - 261
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:481 OR RESID 604:604 OR RESID 606:606 ) )A350 - 481
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:481 OR RESID 604:604 OR RESID 606:606 ) )A604
8X-RAY DIFFRACTION3( CHAIN A AND ( RESID 119:261 OR RESID 350:481 OR RESID 604:604 OR RESID 606:606 ) )A606
9X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 604:604 OR RESID 606:606 ) )B119 - 260
10X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 604:604 OR RESID 606:606 ) )B350 - 480
11X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 604:604 OR RESID 606:606 ) )B604
12X-RAY DIFFRACTION4( CHAIN B AND ( RESID 119:260 OR RESID 350:480 OR RESID 604:604 OR RESID 606:606 ) )B606
13X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 604:604 OR RESID 607:607 ) )C119 - 261
14X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 604:604 OR RESID 607:607 ) )C351 - 482
15X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 604:604 OR RESID 607:607 ) )C604
16X-RAY DIFFRACTION5( CHAIN C AND ( RESID 119:261 OR RESID 351:482 OR RESID 604:604 OR RESID 607:607 ) )C607
17X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 603:603 OR RESID 604:604 ) )D119 - 261
18X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 603:603 OR RESID 604:604 ) )D351 - 482
19X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 603:603 OR RESID 604:604 ) )D603
20X-RAY DIFFRACTION6( CHAIN D AND ( RESID 119:261 OR RESID 351:482 OR RESID 603:603 OR RESID 604:604 ) )D604
21X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B261 - 349
22X-RAY DIFFRACTION7( CHAIN B AND ( RESID 261:349 OR RESID 481:564 ) )B481 - 564
23X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C262 - 350
24X-RAY DIFFRACTION8( CHAIN C AND ( RESID 262:350 OR RESID 483:564 ) )C483 - 564

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