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- PDB-3c85: Crystal structure of TrkA domain of putative glutathione-regulate... -

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Basic information

Entry
Database: PDB / ID: 3c85
TitleCrystal structure of TrkA domain of putative glutathione-regulated potassium-efflux KefB from Vibrio parahaemolyticus
ComponentsPutative glutathione-regulated potassium-efflux system protein KefB
KeywordsTRANSPORT PROTEIN / TrkA domain / putative glutathione-regulated potassium-efflux KefB / Vibrio parahaemolyticus / PSI-2 / Protein Structure Initiative / Structural Genomics / Midwest Center for Structural Genomics / MCSG / Transmembrane / Transport
Function / homology
Function and homology information


antiporter activity / proton transmembrane transport / potassium ion transport / nucleotide binding / membrane
Similarity search - Function
Sodium/solute symporter superfamily / TrkA-N domain / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / Regulator of K+ conductance, N-terminal / RCK N-terminal domain profile. / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Putative glutathione-regulated potassium-efflux system protein KefB
Similarity search - Component
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWu, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of TrkA domain of putative glutathione-regulated potassium-efflux KefB from Vibrio parahaemolyticus.
Authors: Wu, R. / Abdullah, J. / Joachimiak, A.
History
DepositionFeb 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Putative glutathione-regulated potassium-efflux system protein KefB
B: Putative glutathione-regulated potassium-efflux system protein KefB
C: Putative glutathione-regulated potassium-efflux system protein KefB
D: Putative glutathione-regulated potassium-efflux system protein KefB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5427
Polymers82,0034
Non-polymers5393
Water4,828268
1
A: Putative glutathione-regulated potassium-efflux system protein KefB
C: Putative glutathione-regulated potassium-efflux system protein KefB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4454
Polymers41,0012
Non-polymers4432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
MethodPISA
2
B: Putative glutathione-regulated potassium-efflux system protein KefB
D: Putative glutathione-regulated potassium-efflux system protein KefB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0973
Polymers41,0012
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.733, 66.382, 145.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative glutathione-regulated potassium-efflux system protein KefB


Mass: 20500.682 Da / Num. of mol.: 4 / Fragment: Residues 350-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VP0827 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87RG9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 25% PEG 3350, 0.5M KCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2007 / Details: Mirrors
RadiationMonochromator: Si(111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. all: 118442 / Num. obs: 111690 / % possible obs: 91.9 % / Redundancy: 4.5 % / Biso Wilson estimate: 29.41 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.6
Reflection shellResolution: 1.73→1.8 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.059 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→31.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.43 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23221 2377 5.1 %RANDOM
Rwork0.1897 ---
obs0.19191 44205 92.85 %-
all-44205 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.151 Å2
Baniso -1Baniso -2Baniso -3
1-2.13 Å20 Å20 Å2
2---1.28 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→31.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 33 268 4563
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214418
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.9635970
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.9555555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.82324.152224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40915745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7151537
X-RAY DIFFRACTIONr_chiral_restr0.1150.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023414
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.21965
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22966
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.295
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4521.52740
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.39424343
X-RAY DIFFRACTIONr_scbond_it3.65331678
X-RAY DIFFRACTIONr_scangle_it5.3794.51627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 161 -
Rwork0.217 3161 -
obs--91.34 %
Refinement TLS params.Method: refined / Origin x: 17.4651 Å / Origin y: 32.5182 Å / Origin z: 36.7549 Å
111213212223313233
T-0.0118 Å20.0056 Å2-0.0054 Å2--0.0211 Å2-0.0017 Å2---0.0055 Å2
L0.151 °20.0793 °2-0.1041 °2-0.0903 °2-0.072 °2--0.1354 °2
S-0.0044 Å °0.0125 Å °0.0001 Å °-0.004 Å °0.0064 Å °-0.0091 Å °0.0017 Å °0.0016 Å °-0.002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA29 - 17833 - 182
2X-RAY DIFFRACTION1BB30 - 17334 - 177
3X-RAY DIFFRACTION1CC30 - 17534 - 179
4X-RAY DIFFRACTION1DD36 - 17940 - 183

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