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- PDB-5g3q: Crystal structure of a hypothetical domain in WNK1 -

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Basic information

Entry
Database: PDB / ID: 5g3q
TitleCrystal structure of a hypothetical domain in WNK1
ComponentsWNK1
KeywordsTRANSFERASE / DE NOVO PROTEIN
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.613 Å
AuthorsPinkas, D.M. / Bufton, J.C. / Sanvitale, C.E. / Bartual, S.G. / Adamson, R.J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Pinkas, D.M. / Bufton, J.C. / Sanvitale, C.E. / Bartual, S.G. / Adamson, R.J. / Krojer, T. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: To be Published
Title: Crystal Structure of a Hypothetical Domain in Wnk1
Authors: Pinkas, D.M. / Bufton, J.C. / Sanvitale, C.E. / Bartual, S.G. / Adamson, R.J. / Burgess-Brown, N.A. / Krojer, T. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionApr 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Structure summary / Category: entity / struct_keywords
Item: _entity.pdbx_description / _struct_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WNK1
B: WNK1


Theoretical massNumber of molelcules
Total (without water)20,5632
Polymers20,5632
Non-polymers00
Water2,630146
1
A: WNK1


Theoretical massNumber of molelcules
Total (without water)10,2821
Polymers10,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: WNK1


Theoretical massNumber of molelcules
Total (without water)10,2821
Polymers10,2821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.238, 70.324, 82.255
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 WNK1


Mass: 10281.576 Da / Num. of mol.: 2 / Fragment: HYPOTHETICAL DOMAIN, RESIDUES 1113-1201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.76 Å3/Da / Density % sol: 55.43 % / Description: NONE
Crystal growDetails: 20% PEG3350 -- 10% ETHYLENE GLYCOL -- 0.1M BIS-TRIS-PROPANE PH 6.5 -- 0.2M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.61→82.3 Å / Num. obs: 30010 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 27
Reflection shellResolution: 1.61→1.62 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNRELEASED SAD-DETERMINED SELENOMETHIOINE MODEL

Resolution: 1.613→35.502 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2236 1513 5.1 %
Rwork0.2016 --
obs0.2028 29952 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.613→35.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 146 1503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181370
X-RAY DIFFRACTIONf_angle_d1.6211843
X-RAY DIFFRACTIONf_dihedral_angle_d15.244540
X-RAY DIFFRACTIONf_chiral_restr0.086213
X-RAY DIFFRACTIONf_plane_restr0.008247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6132-1.66530.31791290.262534X-RAY DIFFRACTION100
1.6653-1.72480.31651110.2482577X-RAY DIFFRACTION100
1.7248-1.79390.28861420.24232552X-RAY DIFFRACTION100
1.7939-1.87550.27961440.22982544X-RAY DIFFRACTION100
1.8755-1.97440.26091480.21922550X-RAY DIFFRACTION100
1.9744-2.09810.25231380.21272547X-RAY DIFFRACTION100
2.0981-2.260.211420.20272578X-RAY DIFFRACTION100
2.26-2.48740.22371200.19322593X-RAY DIFFRACTION99
2.4874-2.84720.24351350.20312622X-RAY DIFFRACTION100
2.8472-3.58660.21361510.20232620X-RAY DIFFRACTION100
3.5866-35.51050.2061530.1912722X-RAY DIFFRACTION99

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