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- PDB-5yhu: Crystal structure of the DNA-binding domain of human myelin-gene ... -

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Basic information

Entry
Database: PDB / ID: 5yhu
TitleCrystal structure of the DNA-binding domain of human myelin-gene regulatory factor
ComponentsMyelin regulatory factor
KeywordsTRANSCRIPTION / myelingene regulatory factor / DNA-binding domain
Function / homology
Function and homology information


central nervous system myelin maintenance / central nervous system myelination / positive regulation of myelination / oligodendrocyte development / Hydrolases; Acting on peptide bonds (peptidases) / oligodendrocyte differentiation / protein autoprocessing / peptidase activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...central nervous system myelin maintenance / central nervous system myelination / positive regulation of myelination / oligodendrocyte development / Hydrolases; Acting on peptide bonds (peptidases) / oligodendrocyte differentiation / protein autoprocessing / peptidase activity / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Myelin gene regulatory factor C-terminal domain 2 / Myelin gene regulatory factor, ICA domain / Myelin regulatory factor ICA domain / Myelin gene regulatory factor C-terminal domain 2 / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain ...Myelin gene regulatory factor C-terminal domain 2 / Myelin gene regulatory factor, ICA domain / Myelin regulatory factor ICA domain / Myelin gene regulatory factor C-terminal domain 2 / NDT80 DNA-binding domain / NDT80 DNA-binding domain superfamily / NDT80 / PhoG like DNA-binding family / NDT80 DNA-binding domain profile. / Chaperone of endosialidase / Intramolecular chaperone auto-processing domain / Intramolecular chaperone auto-processing (ICA) domain profile. / p53-like transcription factor, DNA-binding
Similarity search - Domain/homology
Myelin regulatory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsChen, B. / Zhu, Y. / Ye, S. / Zhang, R.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Structure of the DNA-binding domain of human myelin-gene regulatory factor reveals its potential protein-DNA recognition mode.
Authors: Chen, B. / Zhu, Y. / Ye, S. / Zhang, R.
History
DepositionSep 30, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Myelin regulatory factor
B: Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)57,7052
Polymers57,7052
Non-polymers00
Water5,044280
1
A: Myelin regulatory factor

A: Myelin regulatory factor

A: Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)86,5573
Polymers86,5573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4950 Å2
ΔGint-16 kcal/mol
Surface area26800 Å2
MethodPISA
2
B: Myelin regulatory factor

B: Myelin regulatory factor

B: Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)86,5573
Polymers86,5573
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area5080 Å2
ΔGint-13 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.122, 105.122, 297.413
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-612-

HOH

21A-647-

HOH

31A-748-

HOH

41A-753-

HOH

51A-790-

HOH

61A-843-

HOH

71A-844-

HOH

81B-609-

HOH

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Components

#1: Protein Myelin regulatory factor / Myelin gene regulatory factor


Mass: 28852.494 Da / Num. of mol.: 2 / Fragment: DNA-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYRF, C11orf9, KIAA0954, MRF / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2G1, Hydrolases; Acting on peptide bonds (peptidases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 200mM Calcium acetate, 100mM Tris-HCl pH 7.1, 19% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.85→34.2 Å / Num. obs: 54003 / % possible obs: 99.4 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.6
Reflection shellHighest resolution: 1.85 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.7 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→34.181 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.58
RfactorNum. reflection% reflection
Rfree0.2275 2746 5.08 %
Rwork0.2039 --
obs0.2051 54003 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→34.181 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 0 280 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093099
X-RAY DIFFRACTIONf_angle_d0.9484202
X-RAY DIFFRACTIONf_dihedral_angle_d5.1581881
X-RAY DIFFRACTIONf_chiral_restr0.066453
X-RAY DIFFRACTIONf_plane_restr0.006547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88190.3391230.29442446X-RAY DIFFRACTION96
1.8819-1.91610.37061470.33282477X-RAY DIFFRACTION99
1.9161-1.9530.35061380.29782541X-RAY DIFFRACTION100
1.953-1.99290.22721410.23432562X-RAY DIFFRACTION100
1.9929-2.03620.24991440.2122570X-RAY DIFFRACTION100
2.0362-2.08350.21751280.21072543X-RAY DIFFRACTION100
2.0835-2.13560.21671410.21172539X-RAY DIFFRACTION100
2.1356-2.19340.26981390.21232595X-RAY DIFFRACTION100
2.1934-2.25790.25781420.23552524X-RAY DIFFRACTION100
2.2579-2.33080.24371220.23272599X-RAY DIFFRACTION100
2.3308-2.4140.25571320.22032510X-RAY DIFFRACTION98
2.414-2.51070.24631370.2292546X-RAY DIFFRACTION100
2.5107-2.62490.251410.21252584X-RAY DIFFRACTION100
2.6249-2.76320.22691370.222582X-RAY DIFFRACTION100
2.7632-2.93630.261350.22772566X-RAY DIFFRACTION100
2.9363-3.16280.22791570.20782573X-RAY DIFFRACTION100
3.1628-3.48080.21871370.19862556X-RAY DIFFRACTION98
3.4808-3.98390.22851360.18532598X-RAY DIFFRACTION99
3.9839-5.01670.16611470.1592639X-RAY DIFFRACTION100
5.0167-34.18710.22121220.19592707X-RAY DIFFRACTION98

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