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- PDB-2vpk: Crystal structure of the BTB domain of human myoneurin -

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Basic information

Entry
Database: PDB / ID: 2vpk
TitleCrystal structure of the BTB domain of human myoneurin
ComponentsMYONEURIN
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / METAL-BINDING / ALTERNATIVE SPLICING / ZINC / NUCLEUS / BTB DOMAIN / ZINC-FINGER / DNA-BINDING
Function / homology
Function and homology information


cellular response to leukemia inhibitory factor / DNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCooper, C.D.O. / Murray, J.W. / Bullock, A. / Pike, A.C.W. / von Delft, F. / Filippakopoulos, P. / Salah, E. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. ...Cooper, C.D.O. / Murray, J.W. / Bullock, A. / Pike, A.C.W. / von Delft, F. / Filippakopoulos, P. / Salah, E. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Btb Domain of Human Myoneurin
Authors: Cooper, C.D.O. / Murray, J.W. / Bullock, A. / Pike, A.C.W. / von Delft, F. / Filippakopoulos, P. / Salah, E. / Edwards, A. / Arrowsmith, C.H. / Bountra, C. / Weigelt, J. / Knapp, S.
History
DepositionFeb 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYONEURIN


Theoretical massNumber of molelcules
Total (without water)13,4571
Polymers13,4571
Non-polymers00
Water91951
1
A: MYONEURIN

A: MYONEURIN


Theoretical massNumber of molelcules
Total (without water)26,9142
Polymers26,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area3140 Å2
ΔGint-19 kcal/mol
Surface area14040 Å2
MethodPQS
Unit cell
Length a, b, c (Å)55.688, 55.688, 126.201
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2011-

HOH

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Components

#1: Protein MYONEURIN / BTB DOMAIN OF MYONEURIN / ZINC FINGER / BTB DOMAIN-CONTAINING PROTEIN 31


Mass: 13457.242 Da / Num. of mol.: 1 / Fragment: BTB DOMAIN, RESIDUES 4-117
Source method: isolated from a genetically manipulated source
Details: INTERMOLECULAR DISULFIDE LINK BETWEEN SYMMETRY RELATED CYS6.
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: NEUROMUSCULAR SYSTEM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-RARE2 / References: UniProt: Q9NPC7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.88 Å3/Da / Density % sol: 41.39 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M NA/KPO4, 0.1 M BIS-TRIS PROPANE PH 6.5, 20% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9828
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9828 Å / Relative weight: 1
ReflectionResolution: 1.9→48 Å / Num. obs: 9485 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.33 % / Biso Wilson estimate: 24.33 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 0
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.06 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.4 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IF5

2if5


Resolution: 2→38.317 Å / SU ML: 0.29 / σ(F): 0.05 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 529 6.8 %
Rwork0.1938 --
obs0.1981 7785 92.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.17 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 33.57 Å2
Baniso -1Baniso -2Baniso -3
1-5.4584 Å20 Å20 Å2
2--5.4584 Å20 Å2
3----10.9169 Å2
Refinement stepCycle: LAST / Resolution: 2→38.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 51 979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081842
X-RAY DIFFRACTIONf_angle_d0.9043306
X-RAY DIFFRACTIONf_dihedral_angle_d16.372449
X-RAY DIFFRACTIONf_chiral_restr0.07140
X-RAY DIFFRACTIONf_plane_restr0.004289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.20130.31561190.2411696X-RAY DIFFRACTION90
2.2013-2.51970.26821280.19881759X-RAY DIFFRACTION92
2.5197-3.17440.26461450.171822X-RAY DIFFRACTION95
3.1744-38.32450.23811370.19121979X-RAY DIFFRACTION94
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)
10.453-0.1877-0.23120.4960.28341.2535-0.09640.2917-0.3101-0.02020.24350.4044-0.0892-0.63560.02330.1769-0.0157-0.0280.25770.00750.2335.855118.093824.2669
20.4038-0.6805-0.08761.4670.60091.2501-0.04980.01910.108-0.10370.06270.0302-0.02920.13580.05840.0770.0371-0.01150.14240.02490.138916.114229.739212.1646
30.8211-0.1124-0.35351.26550.48761.09590.08550.1357-0.0365-0.2722-0.0449-0.1316-0.1475-0.42410.01970.2070.0448-0.00540.24480.02110.150212.351726.04554.1687
40.70660.22740.05081.0980.0513-0.1835-0.10550.4876-0.2214-0.7340.08810.3194-0.12010.0604-0.04240.22730.0534-0.04020.2299-0.04890.197113.216816.2582-1.0666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:57)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 58:88)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 89:116)

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