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- PDB-3ree: Crystal structure of mitoNEET -

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Basic information

Entry
Database: PDB / ID: 3ree
TitleCrystal structure of mitoNEET
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / mitoNEET / FeS cluster / FeS
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
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsFunk, M.O. / Arif, W. / Xu, S. / Mueser, T.C.
CitationJournal: Biochemistry / Year: 2011
Title: Complexes of the Outer Mitochondrial Membrane Protein MitoNEET with Resveratrol-3-Sulfate.
Authors: Arif, W. / Xu, S. / Isailovic, D. / Geldenhuys, W.J. / Carroll, R.T. / Funk, M.O.
History
DepositionApr 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9512
Polymers9,7751
Non-polymers1761
Water1,40578
1
A: CDGSH iron-sulfur domain-containing protein 1
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)19,9024
Polymers19,5512
Non-polymers3522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area4620 Å2
ΔGint-54 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.640, 58.640, 177.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-4-

HOH

21A-156-

HOH

31A-157-

HOH

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Components

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


Mass: 9775.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CISD1, C10orf70, ZCD1, MDS029 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3.9 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown by mixing 1 microliter of mitoNEET 23.3 mg/mL in 50 mM Tris HCl, 0.3 M NaCl, pH 8.5 with 1 microliter of 0.1 M Tris HCl, 1.5 ~ 1.8 M ammonium sulfate, pH 8.5 solution ...Details: Crystals were grown by mixing 1 microliter of mitoNEET 23.3 mg/mL in 50 mM Tris HCl, 0.3 M NaCl, pH 8.5 with 1 microliter of 0.1 M Tris HCl, 1.5 ~ 1.8 M ammonium sulfate, pH 8.5 solution against the same solution. Crystals were appeared in 3 days and flash frozen by transfering into 0.1 M Tris HCl, 1.5 ~ 1.8 M amomnium acete, pH 8.5, 20% xylitol for a few minutes, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.76→55.684 Å / Num. all: 15831 / Num. obs: 15831 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rsym value: 0.078 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.76-1.866.60.5141.51489722570.514100
1.86-1.9770.332.31514021580.33100
1.97-2.170.2113.61426020310.211100
2.1-2.2770.1544.71324418860.154100
2.27-2.4970.1165.81225017460.116100
2.49-2.7870.0778.31131416190.07799.9
2.78-3.2170.05710.8992914210.05799.8
3.21-3.946.90.0688830312050.06899.6
3.94-5.576.80.05810.464709500.05899.1
5.57-30.3826.20.03617.234765580.03696.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å30.38 Å
Translation1.98 Å30.38 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QD0

2qd0


Resolution: 1.76→29.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2327 / WRfactor Rwork: 0.2074 / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8529 / SU B: 1.866 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0863 / SU Rfree: 0.0882 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 789 5 %RANDOM
Rwork0.2019 ---
all0.2032 15856 --
obs0.2032 15766 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.3 Å2 / Biso mean: 28.5501 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms610 0 4 78 692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.022629
X-RAY DIFFRACTIONr_bond_other_d0.0030.02452
X-RAY DIFFRACTIONr_angle_refined_deg2.571.933840
X-RAY DIFFRACTIONr_angle_other_deg1.14631097
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.26573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.89723.7532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.47115120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.316154
X-RAY DIFFRACTIONr_chiral_restr0.1680.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02129
X-RAY DIFFRACTIONr_mcbond_it1.8491.5368
X-RAY DIFFRACTIONr_mcbond_other0.5831.5148
X-RAY DIFFRACTIONr_mcangle_it2.7912593
X-RAY DIFFRACTIONr_scbond_it3.973261
X-RAY DIFFRACTIONr_scangle_it6.2284.5245
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 56 -
Rwork0.292 1085 -
all-1141 -
obs-1085 99.65 %

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