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- PDB-4ezf: The Crystal Structure of a Human MitoNEET mutant with an Ala inse... -

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Basic information

Entry
Database: PDB / ID: 4ezf
TitleThe Crystal Structure of a Human MitoNEET mutant with an Ala inserted between Asp 67 and Lys 68
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / 2FE-2S PROTEINS / MEMBRANE / MITOCHONDRION / SIGNAL-ANCHOR / TRANSMEMBRANE / mitoNEET / protein frustration / CDGSH IRON SULFUR DOMAIN-CONTAINING PROTEIN 1 / MITOCHONDRIAL OUTER MEMBRANE
Function / homology
Function and homology information


protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / regulation of cellular respiration / regulation of autophagy / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial outer membrane / protein homodimerization activity / mitochondrion ...protein maturation by [2Fe-2S] cluster transfer / cysteine transaminase / L-cysteine transaminase activity / 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 / molecular replacement / Resolution: 1.19 Å
AuthorsBaxter, E.L. / Zuris, J.A. / Wang, C. / Axelrod, H.L. / Cohen, A.E. / Paddock, M.L. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Allosteric control in a metalloprotein dramatically alters function.
Authors: Baxter, E.L. / Zuris, J.A. / Wang, C. / Vo, P.L. / Axelrod, H.L. / Cohen, A.E. / Paddock, M.L. / Nechushtai, R. / Onuchic, J.N. / Jennings, P.A.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

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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)18,3904
Polymers18,0392
Non-polymers3522
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-17 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.626, 55.356, 58.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 9019.403 Da / Num. of mol.: 2
Fragment: Water-soluble domain, mitoNEET, UNP residues 33-108
Mutation: Ala residue inserted between Asp 67 and Lys 68
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf70, CISD1, MDS029, mitoNEET, ZCD1 / Production host: Escherichia coli (E. coli) / Strain (production host): B21-RIL / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 1.79 Å3/Da / Density % sol: 31.33 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 6, 2010 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionHighest resolution: 1.19 Å / Num. obs: 41819 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.933 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.19-1.230.7911.9819355354589.8
1.23-1.280.6872.931453414997.4
1.28-1.340.5874.18429404298100
1.34-1.410.3856.24418344153100
1.41-1.50.2658.88430304260100
1.5-1.610.16114.07407414009100
1.61-1.780.09122.75453344447100
1.78-2.030.05834.17418744136100
2.03-2.560.04445.91431764333100
2.560.02855.6242452448999.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.82 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å32.88 Å
Translation2 Å32.88 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2QH7

2qh7


Resolution: 1.19→40.35 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.12 / σ(F): 1.38 / Phase error: 15.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1671 2111 5.06 %
Rwork0.1646 --
obs0.1647 41740 98.69 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.807 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 45.19 Å2 / Biso mean: 19.2458 Å2 / Biso min: 9.69 Å2
Baniso -1Baniso -2Baniso -3
1-3.6609 Å20 Å2-0 Å2
2--1.0445 Å2-0 Å2
3----4.7054 Å2
Refinement stepCycle: LAST / Resolution: 1.19→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 8 133 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091201
X-RAY DIFFRACTIONf_angle_d1.6681622
X-RAY DIFFRACTIONf_chiral_restr0.079169
X-RAY DIFFRACTIONf_plane_restr0.008212
X-RAY DIFFRACTIONf_dihedral_angle_d13.238460
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.19-1.21770.2671170.28262346246388
1.2177-1.24810.28021470.22282466261394
1.2481-1.28190.19391430.19622607275099
1.2819-1.31960.17531330.171326492782100
1.3196-1.36220.17281330.151726502783100
1.3622-1.41090.16271390.134226472786100
1.4109-1.46740.15881450.122126342779100
1.4674-1.53420.14521230.116926632786100
1.5342-1.61510.12281560.110626642820100
1.6151-1.71620.1291360.108826462782100
1.7162-1.84880.13351350.120327012836100
1.8488-2.03480.13631410.135226892830100
2.0348-2.32920.18441360.156527112847100
2.3292-2.93440.19341710.18627152886100
2.9344-40.36820.16351560.19432841299799

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