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- PDB-4f2c: The Crystal Structure of a Human MitoNEET double mutant in which ... -

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Basic information

Entry
Database: PDB / ID: 4f2c
TitleThe Crystal Structure of a Human MitoNEET double mutant in which Gly 66 are Asp 67 are both Replaced with Ala Residues
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / MITOCHONDRIAL OUTER MEMBRANE / SIGNAL-ANCHOR / TRANSMEMBRANE METAL BINDING PROTEIN / PROTEIN FRUSTRATION
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: 1.35 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 7, 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

Downloads & links

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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)18,1884
Polymers17,8372
Non-polymers3522
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-16 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.632, 51.995, 59.018
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: 8918.343 Da / Num. of mol.: 2 / Fragment: Water-soluble domain, UNP residues 33-108 / Mutation: G66A,D67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf70, CISD1, MDS029, ZCD1 / Plasmid: pET28-a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B21-RIL / References: UniProt: Q9NZ45
#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.: 185 / 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: 1.96 Å3/Da / Density % sol: 37.33 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2009 / Details: Rh coated flat mirror.
RadiationMonochromator: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→39.014 Å / Num. all: 31045 / Num. obs: 31045 / % possible obs: 98.3 % / Redundancy: 9.2 % / Rsym value: 0.069 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.35-1.394.50.6571.1889919660.65785.1
1.39-1.425.20.5581.31095420880.55893.6
1.42-1.466.40.4851.51355321330.48598.3
1.46-1.518.20.4541.71719321080.45499.9
1.51-1.5610.40.37622148420600.376100
1.56-1.6110.50.2832.62078119850.283100
1.61-1.6710.40.2263.32017019310.226100
1.67-1.7410.50.1754.21948318620.175100
1.74-1.8210.50.1395.21860217800.139100
1.82-1.9110.40.1136.41787317110.113100
1.91-2.0110.40.0937.51690716190.093100
2.01-2.1310.40.0769.11612915470.076100
2.13-2.2810.30.0699.71509114620.069100
2.28-2.4610.30.06110.81406613620.061100
2.46-2.710.20.05710.81278012570.057100
2.7-3.0210.10.04812.31160411520.048100
3.02-3.499.70.03516.4995010270.03599.9
3.49-4.279.30.0291880878700.029100
4.27-6.0410.10.03116.470997020.031100
6.04-59.0188.90.03315.837824230.03399.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.88 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å39.01 Å
Translation2.5 Å39.01 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QH7

2qh7


Resolution: 1.35→39.014 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.18 / σ(F): 1.48 / Phase error: 14.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1812 1568 5.06 %
Rwork0.1526 --
obs0.154 30975 98.19 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.466 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 43.46 Å2 / Biso mean: 17.4073 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.1812 Å20 Å2-0 Å2
2--0.9501 Å2-0 Å2
3----1.1312 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1058 0 8 185 1251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081165
X-RAY DIFFRACTIONf_angle_d1.5251577
X-RAY DIFFRACTIONf_chiral_restr0.07165
X-RAY DIFFRACTIONf_plane_restr0.006203
X-RAY DIFFRACTIONf_dihedral_angle_d11.567462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.39360.3418960.3122329242586
1.3936-1.44340.27761430.25232554269795
1.4434-1.50120.20421510.19872642279399
1.5012-1.56950.19781410.145327002841100
1.5695-1.65230.14841580.114326662824100
1.6523-1.75580.14111400.101327092849100
1.7558-1.89130.14161350.113526912826100
1.8913-2.08170.17331570.129727242881100
2.0817-2.38290.16861460.147527272873100
2.3829-3.0020.19531580.160827642922100
3.002-39.03020.18021430.159529013044100

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