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- PDB-5x9c: Crystal structure of the cytosolic domain of human MiD51 -

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Basic information

Entry
Database: PDB / ID: 5x9c
TitleCrystal structure of the cytosolic domain of human MiD51
ComponentsMitochondrial dynamics protein MID51
KeywordsTRANSFERASE / Receptor / Mitochondrial fission / Nucleotidyltransferase fold
Function / homology
Function and homology information


mitochondrial fission / positive regulation of mitochondrial fission / positive regulation of protein targeting to membrane / ADP binding / GDP binding / cellular response to hypoxia / mitochondrial outer membrane / mitochondrion / identical protein binding
Similarity search - Function
Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal domain / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like ...Mitochondrial dynamics protein MID49/MID51 / : / Mitochondrial dynamics protein MID51-like, C-terminal domain / Beta Polymerase; domain 2 - #90 / Poly(a)-polymerase, middle domain - #40 / Poly(a)-polymerase, middle domain / Mab-21-like, HhH/H2TH-like domain / Mab-21 protein HhH/H2TH-like domain / Mab-21 protein nucleotidyltransferase domain / Mab-21-like / Mab-21 / Beta Polymerase; domain 2 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Mitochondrial dynamics protein MIEF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSun, F. / Pang, X. / Ma, J.
Funding support China, 2items
OrganizationGrant numberCountry
the Chinese Ministry of Science and Technology2014CB910700, 2011CB910301 China
the Chinese Academy of ScienceXDB08030202 China
CitationJournal: To Be Published
Title: New interfaces on MiD51 for Drp1 recruitment and mitochondrial fission regulation
Authors: Ma, J. / Zhai, Y. / Chen, M. / Zhang, K. / Shi, Y. / Chen, Q. / Pang, X. / Sun, F.
History
DepositionMar 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Mitochondrial dynamics protein MID51
B: Mitochondrial dynamics protein MID51


Theoretical massNumber of molelcules
Total (without water)74,8942
Polymers74,8942
Non-polymers00
Water3,621201
1
A: Mitochondrial dynamics protein MID51


Theoretical massNumber of molelcules
Total (without water)37,4471
Polymers37,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-6 kcal/mol
Surface area16250 Å2
MethodPISA
2
B: Mitochondrial dynamics protein MID51


Theoretical massNumber of molelcules
Total (without water)37,4471
Polymers37,4471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-6 kcal/mol
Surface area16040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.297, 64.666, 65.914
Angle α, β, γ (deg.)89.81, 108.08, 117.19
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Mitochondrial dynamics protein MID51 / Mitochondrial dynamics protein of 51 kDa


Mass: 37446.996 Da / Num. of mol.: 2 / Fragment: UNP residues 133-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MID51 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NQG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.6 M NaH2PO4/K2HPO4, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→48.54 Å / Num. obs: 68988 / % possible obs: 95.3 % / Redundancy: 5.5 % / Net I/σ(I): 23.9
Reflection shellResolution: 1.86→1.92 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.654 / Mean I/σ(I) obs: 5.4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X9B

5x9b


Resolution: 1.85→48.54 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.232 4258 4.887 %THIN-RESOLUTION SHELLS
Rwork0.203 ---
obs0.205 68988 95.3 %-
Refinement stepCycle: LAST / Resolution: 1.85→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 10 201 5395

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