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- PDB-4gvl: Crystal Structure of the GsuK RCK domain -

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Basic information

Entry
Database: PDB / ID: 4gvl
TitleCrystal Structure of the GsuK RCK domain
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. / Potassium channel domain / Ion channel ...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. / Potassium channel domain / Ion channel / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Plaits / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / TrkA domain protein
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionAug 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)202,36916
Polymers200,5584
Non-polymers1,81112
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-93 kcal/mol
Surface area81810 Å2
MethodPISA
2
A: TrkA domain protein
B: TrkA domain protein
C: TrkA domain protein
D: TrkA domain protein
hetero molecules

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)404,73732
Polymers401,1158
Non-polymers3,62224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area27680 Å2
ΔGint-203 kcal/mol
Surface area158620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.648, 161.693, 310.127
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe complete biological assembly is composed of the same tetramer seen in the asymmetric unit.

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Components

#1: Protein
TrkA domain protein


Mass: 50139.418 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca

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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: 3.46 Å3/Da / Density % sol: 64.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20-23% PEG3350, 120mM KCl, 80mM NaNO3, 1% Glycerol, 100mM Bis-Tris Propane, pH 8.5, 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: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 55435 / Observed criterion σ(I): 1.829
Reflection shellResolution: 3→3.07 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.8299 / Num. unique all: 3440 / % possible all: 93.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNQ Gating Ring

1lnq


Resolution: 3→48.45 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 48.252 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26178 1128 2 %RANDOM
Rwork0.22816 ---
obs0.22886 54224 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 124.639 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---3.62 Å20 Å2
3---3.91 Å2
Refinement stepCycle: LAST / Resolution: 3→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13840 0 100 0 13940
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214184
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9819336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90551816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19223.289596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.389152316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51215128
X-RAY DIFFRACTIONr_chiral_restr0.0780.22320
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210632
X-RAY DIFFRACTIONr_nbd_refined0.2170.26544
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2443
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.2102
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.22
X-RAY DIFFRACTIONr_mcbond_it0.3361.59208
X-RAY DIFFRACTIONr_mcangle_it0.627214628
X-RAY DIFFRACTIONr_scbond_it0.7735381
X-RAY DIFFRACTIONr_scangle_it1.344.54708
LS refinement shellResolution: 2.997→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 70 -
Rwork0.333 3503 -
obs--100 %
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)
12.90770.38931.17314.1870.73644.42770.1126-0.428-0.22580.33860.05261.00520.0107-0.6475-0.1652-0.34950.02010.0327-0.24480.1762-0.40775.8786-58.1124-40.6524
22.43940.1875-0.57063.6596-0.66362.9652-0.0544-0.49080.49250.41220.12950.2384-0.3999-0.2788-0.0751-0.3330.13140.0924-0.2683-0.0987-0.38549.6673-23.0687-46.2263
36.64520.2434-0.34225.0101-1.89654.18460.0045-1.00220.05790.9887-0.0731-0.4982-0.19910.22980.0686-0.03560.0566-0.1091-0.3491-0.4556-0.981637.4462-22.5168-23.7713
45.8438-1.5869-0.43897.59631.39472.91710.268-0.8576-0.72660.43890.00970.21050.1554-0.3951-0.2777-0.13210.0728-0.24830.13020.2575-0.969733.6047-57.3718-18.1467
55.17950.0128-0.14998.94550.62674.87220.01570.0999-0.1061-0.09230.2299-0.78440.06960.1917-0.2455-0.4539-0.007-0.0598-0.3618-0.0278-0.343814.9806-45.7608-67.5907
65.42620.2476-0.65244.37970.35126.2149-0.0388-0.01940.21050.25690.0982-0.07560.05270.2067-0.0595-0.44720.0399-0.019-0.538-0.1365-0.473638.8375-17.1901-54.9181
75.68261.0024-2.56048.9176-3.58346.1185-0.1294-0.34010.0209-0.7555-0.2085-0.85860.2780.330.3379-0.12320.1404-0.2198-0.0976-0.1089-0.426458.3723-43.7789-32.6695
814.3247-1.5935-1.44346.30791.4835.3574-0.11020.4781-0.8603-0.26760.1044-0.48590.06450.3550.0059-0.14850.0557-0.2748-0.24810.0503-0.419333.699-72.6795-45.4905
96.00671.69810.87777.3065-0.55378.3116-0.2195-0.3065-0.006-0.22030.09360.2833-0.2687-0.17680.126-0.47130.0215-0.0503-0.35450.0099-0.464-4.9479-57.5602-76.6783
1013.0197-1.23791.72417.1209-1.39494.0745-0.00090.17830.62920.3982-0.1497-0.3667-0.76510.20960.1505-0.2050.06180.0419-0.4834-0.081-0.247828.90163.7461-64.1103
118.0611-2.1708-0.808711.6885-0.54197.7090.4611-1.20911.34460.7037-0.3077-2.1429-0.40040.9462-0.15340.4371-0.2543-0.73130.8084-0.18960.739973.3769-30.2339-18.2952
1213.4114-3.50625.10857.71451.165512.7459-0.0989-0.74850.05340.32410.19640.70060.04490.1021-0.09740.31170.091-0.12820.05590.05960.138738.7854-92.2074-31.3359
1322.4764-3.5716-1.572914.2997-0.21519.0315-0.2485-0.4313-0.71790.7358-0.03360.80720.5186-0.44440.2821-0.3843-0.14030.0504-0.57880.0095-0.6454-16.8093-73.756-67.0666
146.3267-1.83030.3157.15070.7144.71310.29470.58970.73020.10470.20470.2644-0.63720.0524-0.4994-0.28460.19230.1743-0.30410.0834-0.37478.05998.9105-70.0733
153.19131.8866-1.54161.1153-0.91130.7446-0.6596-0.67961.2341.4455-0.1515-0.1608-1.50231.06760.81122.1813-0.0212-0.56511.2387-0.44371.897571.3884-8.9295-12.2464
1614.9055-8.4396-0.416810.9843-2.508316.1915-1.0815-0.99170.9881.14160.77530.0105-0.3450.66260.3063-0.02270.1912-0.1810.5938-0.2698-0.464447.481-91.9998-10.6044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A110 - 247
2X-RAY DIFFRACTION1A466 - 479
3X-RAY DIFFRACTION2B110 - 247
4X-RAY DIFFRACTION2B466 - 479
5X-RAY DIFFRACTION3C110 - 247
6X-RAY DIFFRACTION3C466 - 479
7X-RAY DIFFRACTION4D110 - 247
8X-RAY DIFFRACTION4D466 - 479
9X-RAY DIFFRACTION5A248 - 261
10X-RAY DIFFRACTION5A351 - 465
11X-RAY DIFFRACTION5A601 - 603
12X-RAY DIFFRACTION6B248 - 261
13X-RAY DIFFRACTION6B351 - 465
14X-RAY DIFFRACTION6B601 - 603
15X-RAY DIFFRACTION7C248 - 261
16X-RAY DIFFRACTION7C351 - 465
17X-RAY DIFFRACTION7C601 - 603
18X-RAY DIFFRACTION8D248 - 261
19X-RAY DIFFRACTION8D351 - 465
20X-RAY DIFFRACTION8A604
21X-RAY DIFFRACTION8D601 - 602
22X-RAY DIFFRACTION9A262 - 350
23X-RAY DIFFRACTION10B262 - 350
24X-RAY DIFFRACTION11C262 - 350
25X-RAY DIFFRACTION12D262 - 350
26X-RAY DIFFRACTION13A480 - 564
27X-RAY DIFFRACTION14B480 - 564
28X-RAY DIFFRACTION15C480 - 564
29X-RAY DIFFRACTION16D480 - 564

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