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- PDB-3s2r: ATChloroNEET (H87C mutant) -

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Basic information

Entry
Database: PDB / ID: 3s2r
TitleATChloroNEET (H87C mutant)
ComponentsAT5g51720/MIO24_14
KeywordsMETAL BINDING PROTEIN / redox / Fe-S cluster
Function / homology
Function and homology information


leaf senescence / plastid / chloroplast stroma / reactive oxygen species metabolic process / chloroplast / regulation of autophagy / 2 iron, 2 sulfur cluster binding / mitochondrion / metal ion binding / cytosol
Similarity search - Function
CDGSH iron-sulfur domain, mitoNEET-type / 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 NEET
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
Authorslivnah, O. / Eisenberg-Domovich, Y. / nechushtai, R.
CitationJournal: To be Published
Title: Arabidopsis thaliana ChloroNEET, a Member of the New NEET Family of Human Proteins, is Involved in Development, Senescence and Iron Metabolism.
Authors: Nechushtai, R. / Conlan, A.R. / Song, L. / Harir, Y. / Yogev, O. / Eisenberg-Domovich, Y. / Livnah, O. / Michaeli, D. / Rosen, R. / Ma, V. / Luo, Y. / Zuris, J.A. / Shulaev, V. / Paddock, M. ...Authors: Nechushtai, R. / Conlan, A.R. / Song, L. / Harir, Y. / Yogev, O. / Eisenberg-Domovich, Y. / Livnah, O. / Michaeli, D. / Rosen, R. / Ma, V. / Luo, Y. / Zuris, J.A. / Shulaev, V. / Paddock, M.L. / Cabantchik, Z.Y. / Jennings, P.A. / Mittler, R.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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: AT5g51720/MIO24_14
B: AT5g51720/MIO24_14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6874
Polymers18,3352
Non-polymers3522
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-46 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.290, 54.105, 72.682
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 AT5g51720/MIO24_14 / Genomic DNA / chromosome 5 / P1 clone:MIO24


Mass: 9167.593 Da / Num. of mol.: 2 / Fragment: UNP residues 30-108
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g51720 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FLI7
#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.: 150 / 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: 1.78 Å3/Da / Density % sol: 31.09 %
Crystal growTemperature: 293 K / pH: 8
Details: 100mM NaCl, 20mM Tris (pH 8.0), 0.02% NaN3, LIQUID DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: OPTICAL HUTCH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionLowest resolution: 43 Å / Num. obs: 43972 / % possible obs: 91.4 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S2Q

3s2q


Resolution: 1.14→26.42 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.237 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2157 5 %RANDOM
Rwork0.186 ---
obs0.187 40725 88.8 %-
all-40725 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2--0.09 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 1.14→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 8 150 1232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221107
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.9771491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4185141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7312544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63515201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.79157
X-RAY DIFFRACTIONr_chiral_restr0.1140.2169
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021809
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7531.5708
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53421145
X-RAY DIFFRACTIONr_scbond_it3.2433399
X-RAY DIFFRACTIONr_scangle_it4.484.5342
X-RAY DIFFRACTIONr_rigid_bond_restr1.73731107
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 156 -
Rwork0.283 2839 -
obs--85.57 %
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)
14.71431.41081.90194.99412.53334.6919-0.09390.25180.2777-0.2878-0.04110.1501-0.2278-0.03250.13490.0810.0243-0.01180.05250.02140.02860.1098.6881.277
23.3149-4.54170.60479.5768-0.31160.8509-0.03420.0067-0.094-0.020.02340.2266-0.0522-0.06550.01080.0572-0.00260.00050.063-0.0070.0094-1.828-1.2683.645
37.0622.0592-1.24282.1742-0.12220.8038-0.08820.139-0.0941-0.12160.04790.07230.0187-0.05240.04030.06710.0127-0.00230.0707-0.03080.03410.35-13.7931.262
41.42560.06220.25741.16130.12660.93140.00650.08250.1742-0.0767-0.0098-0.1084-0.0920.0590.00320.0594-0.01120.01790.05350.00050.036213.0334.6135.638
53.735-2.1475-0.9176.80640.5720.4565-0.0309-0.0677-0.14840.0951-0.0178-0.1096-0.02880.02520.04870.0594-0.00520.00460.0685-0.00810.030313.308-5.9789.759
60.63370.237-1.11392.0324-0.09223.64490.0506-0.03250.06220.11170.01620.0074-0.18050.0088-0.06680.0703-0.0096-0.00330.0557-0.02930.03729.81211.8817.868
71.2390.21740.0531.35920.19030.47720.0347-0.2293-0.0660.0863-0.0372-0.04230.017-0.00640.00250.0595-0.01030.00160.07210.00310.00755.497-3.97515.155
84.72790.90130.3171.1457-0.5966.50570.002-0.01410.28560.16150.06590.1886-0.3559-0.1258-0.06780.11370.020.01810.0788-0.06260.1225-6.3039.913.61
91.9141-0.93570.24060.48130.153.1207-0.0451-0.05450.11620.00230.0104-0.0462-0.1805-0.08690.03470.10090.0053-0.00020.1006-0.03620.1433-2.85410.5858.724
101.89030.8792-0.17453.91670.82091.3553-0.021-0.0405-0.04870.05080.00370.071-0.04620.00670.01730.0598-0.00220.00130.0578-0.00680.00931.247-6.8498.139
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A45 - 53
2X-RAY DIFFRACTION2A54 - 62
3X-RAY DIFFRACTION3A63 - 67
4X-RAY DIFFRACTION4A68 - 101
5X-RAY DIFFRACTION5A102 - 106
6X-RAY DIFFRACTION6B41 - 53
7X-RAY DIFFRACTION7B54 - 88
8X-RAY DIFFRACTION8B89 - 94
9X-RAY DIFFRACTION9B95 - 101
10X-RAY DIFFRACTION10B102 - 106

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