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- PDB-3ew0: The novel 2Fe-2S outer mitochondrial protein mitoNEET displays co... -

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Basic information

Entry
Database: PDB / ID: 3ew0
TitleThe novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain
ComponentsCDGSH iron sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / mitochondrial outer membrane / 2Fe-2S proteins / isotopic labeling / highyield expression / Iron / Iron-sulfur / Membrane / Metal-binding / Mitochondrion / Mitochondrion outer membrane / Signal-anchor / Transmembrane
Function / homology
Function and homology information


cysteine transaminase / L-cysteine transaminase activity / protein maturation by [2Fe-2S] cluster transfer / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion ...cysteine transaminase / L-cysteine transaminase activity / protein maturation by [2Fe-2S] cluster transfer / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding
Similarity search - Function
Iron sulphur domain-containing, mitoNEET, N-terminal / Iron-containing outer mitochondrial membrane protein N-terminus / CDGSH iron-sulfur domain-containing protein 1/2 / Iron-binding zinc finger CDGSH type / Iron-binding zinc finger, CDGSH type / MitoNEET, CDGSH iron-sulfur domain / CDGSH-type zinc finger. Function unknown.
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsConlan, A.R. / Paddock, M.L. / Wiley, S. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Roy, M. / Nechushtai, R. / Jennings, P.A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The novel 2Fe-2S outer mitochondrial protein mitoNEET displays conformational flexibility in its N-terminal cytoplasmic tethering domain.
Authors: Conlan, A.R. / Paddock, M.L. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Wiley, S. / Roy, M. / Nechushtai, R. / Jennings, P.A.
History
DepositionOct 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CDGSH iron sulfur domain-containing protein 1
B: CDGSH iron sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9134
Polymers18,5612
Non-polymers3522
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-50 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.737, 48.476, 59.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CDGSH iron sulfur domain-containing protein 1 / MitoNEET


Mass: 9280.703 Da / Num. of mol.: 2 / Fragment: UNP residues 33-108, WATER-SOLULE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf70, CISD1, MDS029, ZCD1
Plasmid: modified pET28-a(+) vector (Novagen) that contained the superfolder GFP cDNA
Production host: Escherichia coli (E. coli) / Strain (production host): E. coli BL-21(DE3/pET-24d) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 37.33 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8
Details: Crystallization Droplets: 100 mM Tris HCl (pH 8.0), 100 mM NaCl, and 16-18% PEG 3000. Reservoir conditions: 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 30 32% PEG 3000 in the reservoir., VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2007 / Details: Kohzu Dual Double Crystal Monochromator (DDCM)
RadiationMonochromator: double Si(111) crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.4→38.55 Å / Num. all: 26874 / Num. obs: 26874 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rsym value: 0.059 / Net I/σ(I): 19
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.32 / % possible all: 81.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0063refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QH7

2qh7


Resolution: 1.4→38.55 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.027 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.24064 1371 5.1 %RANDOM
Rwork0.19838 ---
obs0.20047 25476 91.34 %-
all-26847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 5.626 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1190 0 8 164 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211265
X-RAY DIFFRACTIONr_bond_other_d0.0010.02858
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9281697
X-RAY DIFFRACTIONr_angle_other_deg0.8453.0062088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.50624.33360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52115213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.226155
X-RAY DIFFRACTIONr_chiral_restr0.0750.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211415
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02258
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_it0.4312772
X-RAY DIFFRACTIONr_mcbond_other0.082314
X-RAY DIFFRACTIONr_mcangle_it0.71231237
X-RAY DIFFRACTIONr_scbond_it0.5442493
X-RAY DIFFRACTIONr_scangle_it0.6393451
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 79 -
Rwork0.252 1557 -
obs--76.81 %
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)
12.93473.33615.564.13966.67110.9060.12820.0507-0.08810.1670.1356-0.20230.21360.1913-0.26380.1462-0.0451-0.020.0567-0.02820.059732.4535.82623.2308
21.2088-0.2221-0.13031.64150.26131.8015-0.01660.0635-0.0091-0.0235-0.050.21050.0755-0.27140.06660.0362-0.0134-0.0160.0845-0.01970.07349.399-2.7225-14.3842
31.31660.1690.36341.80340.15952.28620.0021-0.063-0.09320.0327-0.01910.04130.1937-0.06530.01710.0184-0.00980.00820.0395-0.00210.043113.5056-6.0759-3.45
46.1165-0.4931-10.03473.4219-2.781735.30580.3403-0.24380.2194-0.03670.13120.0848-0.38350.6735-0.47150.0969-0.0706-0.03860.07280.02910.162343.4698-9.879-16.7179
52.27260.8893-1.47251.9015-0.05276.5482-0.0111-0.05720.00080.1125-0.0034-0.06240.02070.36660.01450.00920.0025-0.00730.0650.00070.047721.97020.74853.2526
61.41860.0154-0.75541.49160.18152.92630.0384-0.02050.1133-0.0554-0.05670.1063-0.2461-0.1520.01830.0240.0102-0.00790.0296-0.01820.059912.81526.0635-7.4319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 46
2X-RAY DIFFRACTION2A47 - 68
3X-RAY DIFFRACTION3A69 - 107
4X-RAY DIFFRACTION4B29 - 40
5X-RAY DIFFRACTION5B41 - 55
6X-RAY DIFFRACTION6B56 - 104

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