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- PDB-5zu0: Proteobacterial origin of protein arginine methylation and regula... -

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Basic information

Entry
Database: PDB / ID: 5zu0
TitleProteobacterial origin of protein arginine methylation and regulation of Complex I assembly by MidA
ComponentsProtein arginine methyltransferase NDUFAF7 homolog, mitochondrial
KeywordsTRANSFERASE / MidA / Mitochondrial Complex I / SAM / SAH / Protein Arginine Methyl Transferase
Function / homology
Function and homology information


Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / glutamate metabolic process / protein-arginine omega-N symmetric methyltransferase activity / thermotaxis / sporulation resulting in formation of a cellular spore / glycogen metabolic process ...Complex I biogenesis / pinocytosis / phototaxis / culmination involved in sorocarp development / type II protein arginine methyltransferase / glutamate metabolic process / protein-arginine omega-N symmetric methyltransferase activity / thermotaxis / sporulation resulting in formation of a cellular spore / glycogen metabolic process / positive regulation of mitochondrial fission / mitochondrial respiratory chain complex I assembly / phagocytosis / ATP metabolic process / negative regulation of autophagy / methylation / mitochondrion
Similarity search - Function
Protein arginine methyltransferase NDUFAF7 / Protein arginine methyltransferase NDUFAF7 superfamily / Putative S-adenosyl-L-methionine-dependent methyltransferase / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.76 Å
AuthorsArold, S.T. / Swaminathan, K. / Hameed, U.F.S.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore) Singapore
CitationJournal: Cell Rep / Year: 2018
Title: Proteobacterial Origin of Protein Arginine Methylation and Regulation of Complex I Assembly by MidA.
Authors: Shahul Hameed, U.F.S. / Sanislav, O. / Lay, S.T. / Annesley, S.J. / Jobichen, C. / Fisher, P.R. / Swaminathan, K. / Arold, S.T.
History
DepositionMay 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
B: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
C: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,4916
Polymers142,3383
Non-polymers1,1533
Water3,153175
1
A: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,4461
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,4461
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8302
Polymers47,4461
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.828, 105.163, 201.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SAH / End label comp-ID: SAH / Refine code: _ / Auth seq-ID: 83 - 501 / Label seq-ID: 13

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA - D
21BB - E
12AA - D
22CC - F
13BB - E
23CC - F

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Protein arginine methyltransferase NDUFAF7 homolog, mitochondrial / Mitochondrial dysfunction gene A / NADH dehydrogenase [ubiquinone] complex I / assembly factor 7 homolog


Mass: 47445.855 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: midA, DDB_G0282615 / Production host: Escherichia coli (E. coli)
References: UniProt: Q54S83, type II protein arginine methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M potassium sodium tartrate tetrahydrate, 0.1M BIS-TRIS pH 6.5, 10% w/v polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.9870, 0.9794, 0.9642
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 11, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
20.97941
30.96421
ReflectionResolution: 2.76→100.61 Å / Num. obs: 39759 / % possible obs: 98.09 % / Redundancy: 13.9 % / Rsym value: 0.18 / Net I/σ(I): 12.64
Reflection shellResolution: 2.76→2.86 Å / Num. unique obs: 3811

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2.76→100.61 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.917 / SU B: 25.152 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23583 1975 5 %RANDOM
Rwork0.20006 ---
obs0.20186 37784 98.07 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.353 Å2
Baniso -1Baniso -2Baniso -3
1--3.06 Å2-0 Å20 Å2
2--3.06 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.76→100.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9579 0 78 175 9832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199854
X-RAY DIFFRACTIONr_bond_other_d0.0020.029354
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.98913303
X-RAY DIFFRACTIONr_angle_other_deg0.976321798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81851193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85925.07426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.576151729
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0081533
X-RAY DIFFRACTIONr_chiral_restr0.0950.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110673
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021910
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6173.1434796
X-RAY DIFFRACTIONr_mcbond_other2.6183.1424795
X-RAY DIFFRACTIONr_mcangle_it4.3014.7035981
X-RAY DIFFRACTIONr_mcangle_other4.3014.7055982
X-RAY DIFFRACTIONr_scbond_it3.3113.4465058
X-RAY DIFFRACTIONr_scbond_other3.3113.4475058
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0665.0627322
X-RAY DIFFRACTIONr_long_range_B_refined7.7737.67810691
X-RAY DIFFRACTIONr_long_range_B_other7.76537.64410668
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A252360.09
12B252360.09
21A249700.1
22C249700.1
31B250080.1
32C250080.1
LS refinement shellResolution: 2.762→2.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 143 -
Rwork0.262 2672 -
obs--95.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1646-0.0553-0.14612.163-0.50771.8001-0.10060.1545-0.1156-0.02380.00040.06270.0324-0.07980.10020.3259-0.00380.02370.0776-0.04530.03538.34461.079133.305
21.3261-0.20440.44852.83-0.26721.9583-0.0796-0.05440.08710.04370.1031-0.2342-0.26560.2241-0.02360.27810.0243-0.00740.1336-0.02350.026134.6541.009172.123
32.77190.62570.07362.05540.51971.31570.0798-0.4253-0.00270.3227-0.0318-0.1575-0.01030.0819-0.0480.21170.0218-0.00980.07910.00350.051122.46626.228110.051
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 501
2X-RAY DIFFRACTION2B83 - 501
3X-RAY DIFFRACTION3C83 - 501

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