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- PDB-2w8x: Structure of the tick ion-channel modulator Ra-KLP -

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Basic information

Entry
Database: PDB / ID: 2w8x
TitleStructure of the tick ion-channel modulator Ra-KLP
ComponentsION-CHANNEL MODULATOR RAKLP
KeywordsMEMBRANE PROTEIN / SALIVARY GLAND / KUNITZ DOMAINS / MAXIK CHANNEL ACTIVATION / SULPHUR SAD
Function / homologyPancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Few Secondary Structures / Irregular / ACETATE ION / IMIDAZOLE
Function and homology information
Biological speciesRHIPICEPHALUS APPENDICULATUS (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsPaesen, G.C. / Siebold, C. / Dallas, M. / Peers, C. / Harlos, K. / Nuttall, P.A. / Nunn, M.A. / Stuart, D.I. / Esnouf, R.M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: An Ion-Channel Modulator from the Saliva of the Brown Ear Tick Has a Highly Modified Kunitz/Bpti Structure.
Authors: Paesen, G.C. / Siebold, C. / Dallas, M.L. / Peers, C. / Harlos, K. / Nuttall, P.A. / Nunn, M.A. / Stuart, D.I. / Esnouf, R.M.
History
DepositionJan 20, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ION-CHANNEL MODULATOR RAKLP
B: ION-CHANNEL MODULATOR RAKLP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0595
Polymers16,8392
Non-polymers2203
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-5 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.349, 65.687, 38.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2023-

HOH

21A-2054-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.2478, -0.17277, -0.95328), (-0.16861, -0.97664, 0.13317), (-0.95403, 0.12774, -0.27114)
Vector: 10.17, 19.41, 9.85)

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Components

#1: Protein ION-CHANNEL MODULATOR RAKLP


Mass: 8419.331 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHIPICEPHALUS APPENDICULATUS (arthropod)
Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ORIGAMI(DE3) PLYSS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.93 Å3/Da / Density % sol: 35.91 % / Description: NONE
Crystal growpH: 7.5 / Details: 10% (V/V) ETHANOL, 1.5M NACL, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 23817 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 40.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 62.8
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 18.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
ACORNphasing
ARP/wARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.045 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 736 3.7 %RANDOM
Rwork0.139 ---
obs0.14 19062 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: 13.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 15 162 1284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021213
X-RAY DIFFRACTIONr_bond_other_d0.0010.02875
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9071639
X-RAY DIFFRACTIONr_angle_other_deg0.8933.0162061
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.81222.32973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62915199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.191518
X-RAY DIFFRACTIONr_chiral_restr0.090.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021435
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02283
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4151.5728
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.35721163
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6073485
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6714.5476
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.153 65
Rwork0.116 1364

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