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- PDB-4oo7: THE 1.55A CRYSTAL STRUCTURE of NAF1 (MINER1): THE REDOX-ACTIVE 2F... -

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Basic information

Entry
Database: PDB / ID: 4oo7
TitleTHE 1.55A CRYSTAL STRUCTURE of NAF1 (MINER1): THE REDOX-ACTIVE 2FE-2S PROTEIN
ComponentsCDGSH iron-sulfur domain-containing protein 2
KeywordsMETAL BINDING PROTEIN / MEMBRANE BOUND / THIAZOLIDINEDIONE / OXIDATIVE STRESS
Function / homology
Function and homology information


perinuclear endoplasmic reticulum / regulation of autophagy / autophagy / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding ...perinuclear endoplasmic reticulum / regulation of autophagy / autophagy / 2 iron, 2 sulfur cluster binding / mitochondrial outer membrane / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / RNA binding / membrane / metal ion binding
Similarity search - Function
CDGSH iron-sulfur domain, mitoNEET-type / 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. / Ribosomal Protein L9; domain 1 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CDGSH iron-sulfur domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.65 Å
AuthorsTamir, S. / Eisenberg-Domovich, Y. / Colman, A.R. / Stofleth, J.T. / Lipper, C.H. / Paddock, M.L. / Jenning, P.A. / Livnah, O. / Nechushtai, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A point mutation in the [2Fe-2S] cluster binding region of the NAF-1 protein (H114C) dramatically hinders the cluster donor properties.
Authors: Tamir, S. / Eisenberg-Domovich, Y. / Conlan, A.R. / Stofleth, J.T. / Lipper, C.H. / Paddock, M.L. / Mittler, R. / Jennings, P.A. / Livnah, O. / Nechushtai, R.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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 / _struct_ncs_dom_lim.end_label_seq_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

Downloads & links

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Assembly

Deposited unit
A: CDGSH iron-sulfur domain-containing protein 2
B: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7354
Polymers15,3842
Non-polymers3522
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-46 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.009, 48.652, 73.730
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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 69 - 131 / Label seq-ID: 2 - 64

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein CDGSH iron-sulfur domain-containing protein 2 / Endoplasmic reticulum intermembrane small protein / MitoNEET-related 1 protein / Miner1 / Nutrient- ...Endoplasmic reticulum intermembrane small protein / MitoNEET-related 1 protein / Miner1 / Nutrient-deprivation autophagy factor-1 / NAF-1


Mass: 7691.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CISD2, CDGSH2, ERIS, ZCD2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N5K1
#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.: 87 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 35% PEG 3350, 0.1M Tris-HCL pH 8.0 and 50mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2012
RadiationMonochromator: optical hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 21634 / Num. obs: 21634 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.65→31.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.434 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15043 870 5.1 %RANDOM
Rwork0.13477 ---
obs0.13553 16326 93.88 %-
all-21634 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.015 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0 Å2
2---0.08 Å2-0 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.65→31.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 8 87 1129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191048
X-RAY DIFFRACTIONr_bond_other_d0.0020.021022
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9691402
X-RAY DIFFRACTIONr_angle_other_deg0.8113.0052346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215129
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8325.81443
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05315192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.038154
X-RAY DIFFRACTIONr_chiral_restr0.0870.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211155
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02217
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_it2.2971.734522
X-RAY DIFFRACTIONr_mcbond_other2.2841.729521
X-RAY DIFFRACTIONr_mcangle_it2.7722.595649
X-RAY DIFFRACTIONr_mcangle_other2.4443.261650
X-RAY DIFFRACTIONr_scbond_it2.9132.124526
X-RAY DIFFRACTIONr_scbond_other2.9462.599514
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.393.691747
X-RAY DIFFRACTIONr_long_range_B_refined3.54118.1111154
X-RAY DIFFRACTIONr_long_range_B_other3.07317.6171126
X-RAY DIFFRACTIONr_rigid_bond_restr8.59232070
X-RAY DIFFRACTIONr_sphericity_free28.743543
X-RAY DIFFRACTIONr_sphericity_bonded8.9152103
Refine LS restraints NCS

Ens-ID: 1 / Number: 3110 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.173 43 -
Rwork0.154 763 -
obs--61.15 %

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