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- PDB-4ooa: CRYSTAL STRUCTURE of NAF1 (MINER1): H114C THE REDOX-ACTIVE 2FE-2S... -

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Basic information

Entry
Database: PDB / ID: 4ooa
TitleCRYSTAL STRUCTURE of NAF1 (MINER1): H114C 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: 1.58 Å
AuthorsTamir, 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.
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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

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
C: CDGSH iron-sulfur domain-containing protein 2
D: CDGSH iron-sulfur domain-containing protein 2
E: CDGSH iron-sulfur domain-containing protein 2
F: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,99612
Polymers45,9416
Non-polymers1,0556
Water4,756264
1
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)15,6654
Polymers15,3142
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-44 kcal/mol
Surface area7370 Å2
MethodPISA
2
C: CDGSH iron-sulfur domain-containing protein 2
D: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6654
Polymers15,3142
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-48 kcal/mol
Surface area6990 Å2
MethodPISA
3
E: CDGSH iron-sulfur domain-containing protein 2
F: CDGSH iron-sulfur domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6654
Polymers15,3142
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-46 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.393, 60.985, 135.241
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 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: 7656.838 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 35% PEG 3500, 100 mM Tris-HCl pH 8.0 and 100-200 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2013
RadiationMonochromator: Optical Hutch / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 54202 / Num. obs: 54202 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→30.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.159 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19605 2689 5.1 %RANDOM
Rwork0.15972 ---
obs0.16156 50138 95.11 %-
all-46700 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.58→30.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3070 0 24 264 3358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0193125
X-RAY DIFFRACTIONr_bond_other_d0.0010.023051
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9794188
X-RAY DIFFRACTIONr_angle_other_deg0.7683.0077022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76126.25128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01915584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.0931512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2482
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
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_it1.9931.8031566
X-RAY DIFFRACTIONr_mcbond_other1.9771.81565
X-RAY DIFFRACTIONr_mcangle_it2.4892.6941948
X-RAY DIFFRACTIONr_mcangle_other2.1082.9731949
X-RAY DIFFRACTIONr_scbond_it2.242.031559
X-RAY DIFFRACTIONr_scbond_other2.0422.2281532
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.063.2222219
X-RAY DIFFRACTIONr_long_range_B_refined2.69416.1543576
X-RAY DIFFRACTIONr_long_range_B_other2.49115.7983481
X-RAY DIFFRACTIONr_rigid_bond_restr2.96636176
X-RAY DIFFRACTIONr_sphericity_free22.833573
X-RAY DIFFRACTIONr_sphericity_bonded7.0356296
LS refinement shellResolution: 1.582→1.623 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 153 -
Rwork0.218 2716 -
obs--70.46 %

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