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- PDB-7ydw: Crystal structure of the MPND-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7ydw
TitleCrystal structure of the MPND-DNA complex
Components
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
  • MPN domain-containing protein
KeywordsDNA BINDING PROTEIN / MPND-DNA / COMPLEX
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / metallopeptidase activity / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of transcription by RNA polymerase II / proteolysis / metal ion binding
Similarity search - Function
Restriction enzyme adenine methylase associated / Restriction Enzyme Adenine Methylase Associated / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile.
Similarity search - Domain/homology
DNA / MPN domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsYang, M. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structures of MPND Reveal the Molecular Recognition of Nucleosomes.
Authors: Yang, M. / Li, X. / Tian, Z. / Ma, L. / Ma, J. / Liu, Y. / Shang, G. / Liang, A. / Wu, W. / Chen, Z.
History
DepositionJul 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MPN domain-containing protein
B: MPN domain-containing protein
E: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
C: MPN domain-containing protein
D: MPN domain-containing protein


Theoretical massNumber of molelcules
Total (without water)74,1086
Polymers74,1086
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.783, 62.922, 69.085
Angle α, β, γ (deg.)72.583, 89.876, 89.976
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MPN domain-containing protein


Mass: 17005.990 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mpnd / Production host: Escherichia coli (E. coli)
References: UniProt: Q3TV65, Hydrolases; Acting on peptide bonds (peptidases)
#2: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3087.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 2996.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG4000, sodium citrate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.47→50 Å / Num. obs: 21839 / % possible obs: 96 % / Redundancy: 3.4 % / CC1/2: 0.968 / Net I/σ(I): 9.5
Reflection shellResolution: 2.47→2.51 Å / Mean I/σ(I) obs: 9.5 / Num. unique obs: 899 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YDT

7ydt


Resolution: 2.47→33.44 Å / Cor.coef. Fo:Fc: 0.884 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.245 / SU B: 11.911 / SU ML: 0.246 / Average fsc free: 0.8443 / Average fsc work: 0.8492 / Cross valid method: FREE R-VALUE / ESU R: 0.466 / ESU R Free: 0.268
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2536 1107 5.295 %
Rwork0.2454 19799 -
all0.246 --
obs-20906 95.93 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.658 Å2
Baniso -1Baniso -2Baniso -3
1--2.596 Å2-1.187 Å20.543 Å2
2---5.688 Å2-1.263 Å2
3---6.26 Å2
Refinement stepCycle: LAST / Resolution: 2.47→33.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 409 0 161 3411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123368
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182901
X-RAY DIFFRACTIONr_angle_refined_deg1.1811.574628
X-RAY DIFFRACTIONr_angle_other_deg1.1861.7016700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6915370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76822.821117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63415454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7141513
X-RAY DIFFRACTIONr_chiral_restr0.0440.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined0.1850.2487
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.22124
X-RAY DIFFRACTIONr_nbtor_refined0.1580.21293
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21221
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.28
X-RAY DIFFRACTIONr_nbd_other0.160.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.29
X-RAY DIFFRACTIONr_mcbond_it2.3884.9791489
X-RAY DIFFRACTIONr_mcbond_other2.3884.9771488
X-RAY DIFFRACTIONr_mcangle_it3.9617.4371845
X-RAY DIFFRACTIONr_mcangle_other3.967.4391846
X-RAY DIFFRACTIONr_scbond_it1.9795.3551879
X-RAY DIFFRACTIONr_scbond_other1.9795.3571880
X-RAY DIFFRACTIONr_scangle_it3.4297.9792783
X-RAY DIFFRACTIONr_scangle_other3.4297.9792783
X-RAY DIFFRACTIONr_lrange_it6.07153.7033585
X-RAY DIFFRACTIONr_lrange_other6.05953.6433576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.5340.359880.3461246X-RAY DIFFRACTION81.4408
2.534-2.6030.291730.3521268X-RAY DIFFRACTION87.0214
2.603-2.6790.287590.3121342X-RAY DIFFRACTION92.1105
2.679-2.7610.409700.3171335X-RAY DIFFRACTION94.8683
2.761-2.8510.312820.2931304X-RAY DIFFRACTION97.4684
2.851-2.9510.271830.2531285X-RAY DIFFRACTION98.0645
2.951-3.0620.285740.2391249X-RAY DIFFRACTION98.8789
3.062-3.1860.252700.2341229X-RAY DIFFRACTION98.5584
3.186-3.3270.313580.2391155X-RAY DIFFRACTION98.859
3.327-3.4890.259520.2351124X-RAY DIFFRACTION98.7406
3.489-3.6770.19710.2091032X-RAY DIFFRACTION99.1906
3.677-3.8980.234670.199983X-RAY DIFFRACTION98.8701
3.898-4.1660.176400.178960X-RAY DIFFRACTION99.4036
4.166-4.4970.158520.163864X-RAY DIFFRACTION99.3492
4.497-4.9220.192300.173844X-RAY DIFFRACTION99.3182
4.922-5.4960.156320.181715X-RAY DIFFRACTION99.6
5.496-6.3340.239340.248663X-RAY DIFFRACTION99.7139
6.334-7.7260.343310.287549X-RAY DIFFRACTION99.1453
7.726-100.237310.332408X-RAY DIFFRACTION100
10.799-33.440.72990.681240X-RAY DIFFRACTION96.5116

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