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- PDB-5h5p: Crystal structure of Myelin-gene Regulatory Factor DNA binding domain -

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Basic information

Entry
Database: PDB / ID: 5h5p
TitleCrystal structure of Myelin-gene Regulatory Factor DNA binding domain
ComponentsMyelin regulatory factor
KeywordsTRANSCRIPTION / Ig fold transcription factor / ER membrane protein / trimeric transcription factor
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 / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / Golgi apparatus / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.461 Å
AuthorsShi, N. / Zhen, X. / Li, B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570763 China
Chinese Academy of Sciences100 Talents Program China
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of the DNA-binding domain of Myelin-gene Regulatory Factor.
Authors: Zhen, X. / Li, B. / Hu, F. / Yan, S. / Meloni, G. / Li, H. / Shi, N.
History
DepositionNov 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)21,4961
Polymers21,4961
Non-polymers00
Water37821
1
A: Myelin regulatory factor

A: Myelin regulatory factor

A: Myelin regulatory factor


Theoretical massNumber of molelcules
Total (without water)64,4883
Polymers64,4883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Unit cell
Length a, b, c (Å)103.970, 103.970, 46.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 21495.941 Da / Num. of mol.: 1 / Fragment: UNP residues 351-532
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myrf, Gm1804, Gm98, Mrf / Production host: Escherichia coli (E. coli) / References: UniProt: Q3UR85
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Tris, Magnesium acetate, PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.366→44.95 Å / Num. obs: 24100 / % possible obs: 99.77 % / Redundancy: 8.8 % / Net I/σ(I): 8.52

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.461→34.032 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 2038 9.97 %
Rwork0.1747 --
obs0.1796 20442 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.461→34.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1489 0 0 21 1510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011536
X-RAY DIFFRACTIONf_angle_d1.2092083
X-RAY DIFFRACTIONf_dihedral_angle_d15.895587
X-RAY DIFFRACTIONf_chiral_restr0.048226
X-RAY DIFFRACTIONf_plane_restr0.005272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4606-2.51790.46181230.39091160X-RAY DIFFRACTION95
2.5179-2.58080.3621320.25891253X-RAY DIFFRACTION100
2.5808-2.65060.27831300.22121232X-RAY DIFFRACTION100
2.6506-2.72850.32081320.23561239X-RAY DIFFRACTION100
2.7285-2.81660.27981350.21881245X-RAY DIFFRACTION100
2.8166-2.91720.28261360.23021216X-RAY DIFFRACTION100
2.9172-3.03390.25111380.20651210X-RAY DIFFRACTION100
3.0339-3.17190.271470.19691259X-RAY DIFFRACTION100
3.1719-3.3390.25891360.1831225X-RAY DIFFRACTION100
3.339-3.5480.22651480.16751211X-RAY DIFFRACTION100
3.548-3.82160.22791280.1621238X-RAY DIFFRACTION100
3.8216-4.20550.19131380.14491231X-RAY DIFFRACTION100
4.2055-4.81260.18911320.12951229X-RAY DIFFRACTION100
4.8126-6.05780.1531430.15011225X-RAY DIFFRACTION100
6.0578-34.03540.2071400.17111231X-RAY DIFFRACTION100

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