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- PDB-7ydt: Crystal structure of mouse MPND -

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Basic information

Entry
Database: PDB / ID: 7ydt
TitleCrystal structure of mouse MPND
ComponentsMPN domain containing protein
KeywordsDNA BINDING PROTEIN / MPND
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / metallopeptidase activity / 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
MPN domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.055 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

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Assembly

Deposited unit
A: MPN domain containing protein
B: MPN domain containing protein


Theoretical massNumber of molelcules
Total (without water)34,0122
Polymers34,0122
Non-polymers00
Water1,11762
1
A: MPN domain containing protein


Theoretical massNumber of molelcules
Total (without water)17,0061
Polymers17,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MPN domain containing protein


Theoretical massNumber of molelcules
Total (without water)17,0061
Polymers17,0061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.677, 62.838, 112.619
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein MPN domain containing protein


Mass: 17005.990 Da / Num. of mol.: 2
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.96 Å3/Da / Density % sol: 37.24 % / Description: slice
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Bis Tris, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 17365 / % possible obs: 97.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 13.3
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 732 / CC1/2: 0.883

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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: 6PBD

6pbd


Resolution: 2.055→41.971 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.23 / SU B: 4.897 / SU ML: 0.126 / Average fsc free: 0.8886 / Average fsc work: 0.8981 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.16
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2495 885 5.234 %
Rwork0.2296 16024 -
all0.231 --
obs-16909 97.419 %
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: 34.645 Å2
Baniso -1Baniso -2Baniso -3
1--1.293 Å2-0 Å2-0 Å2
2---2.73 Å20 Å2
3---4.023 Å2
Refinement stepCycle: LAST / Resolution: 2.055→41.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 0 62 1489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171407
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.6361969
X-RAY DIFFRACTIONr_angle_other_deg1.0911.5893228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5135180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.55722.41962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32415249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.337158
X-RAY DIFFRACTIONr_chiral_restr0.0380.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021619
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
X-RAY DIFFRACTIONr_nbd_refined0.1690.2221
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.21103
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2662
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.2616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.261
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.26
X-RAY DIFFRACTIONr_nbd_other0.1620.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.160.23
X-RAY DIFFRACTIONr_mcbond_it1.223.706727
X-RAY DIFFRACTIONr_mcbond_other1.223.704726
X-RAY DIFFRACTIONr_mcangle_it2.0815.54902
X-RAY DIFFRACTIONr_mcangle_other2.0795.543903
X-RAY DIFFRACTIONr_scbond_it1.2023.836733
X-RAY DIFFRACTIONr_scbond_other1.2013.837734
X-RAY DIFFRACTIONr_scangle_it2.0925.671067
X-RAY DIFFRACTIONr_scangle_other2.0915.6711068
X-RAY DIFFRACTIONr_lrange_it3.72540.7491579
X-RAY DIFFRACTIONr_lrange_other3.69340.7061573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.055-2.1080.334640.307965X-RAY DIFFRACTION81.4082
2.108-2.1660.298580.2961024X-RAY DIFFRACTION89.0535
2.166-2.2290.342680.2881091X-RAY DIFFRACTION95.5482
2.229-2.2970.3470.2591087X-RAY DIFFRACTION99.3865
2.297-2.3720.338540.2571066X-RAY DIFFRACTION99.9108
2.372-2.4560.307380.2521048X-RAY DIFFRACTION100
2.456-2.5480.309540.2461000X-RAY DIFFRACTION100
2.548-2.6520.239580.229958X-RAY DIFFRACTION100
2.652-2.770.18560.232916X-RAY DIFFRACTION100
2.77-2.9050.185510.219910X-RAY DIFFRACTION99.896
2.905-3.0610.258490.236834X-RAY DIFFRACTION99.8869
3.061-3.2470.294420.22797X-RAY DIFFRACTION100
3.247-3.470.284560.22757X-RAY DIFFRACTION100
3.47-3.7470.249380.2708X-RAY DIFFRACTION99.4667
3.747-4.1030.235350.196657X-RAY DIFFRACTION100
4.103-4.5850.157400.183597X-RAY DIFFRACTION100
4.585-5.290.182330.181533X-RAY DIFFRACTION99.8236
5.29-6.4670.275250.258468X-RAY DIFFRACTION99.7976
6.467-9.0980.179100.248381X-RAY DIFFRACTION100
9.098-41.9710.51790.333227X-RAY DIFFRACTION95.935

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