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- PDB-4f28: The Crystal Structure of a Human MitoNEET mutant with Met 62 Repl... -

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Basic information

Entry
Database: PDB / ID: 4f28
TitleThe Crystal Structure of a Human MitoNEET mutant with Met 62 Replaced by a Gly
ComponentsCDGSH iron-sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / 2FE-2S PROTEINS / MEMBRANE / SIGNAL-ANCHOR / TRANSMEMBRANE METAL BINDING PROTEIN / PROTEIN FRUSTRATION / MITOCHONDRIAL OUTER MEMBRANE
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: 1.55 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 1.2Feb 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_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)18,1004
Polymers17,7482
Non-polymers3522
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-13 kcal/mol
Surface area6710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.330, 56.600, 59.110
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: 8874.183 Da / Num. of mol.: 2 / Fragment: Water-soluble domain, UNP residues 33-108 / Mutation: M62G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C10orf70, CISD1, MDS029, ZCD1 / 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.: 84 / 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: 1.95 Å3/Da / Density % sol: 36.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 16, 2009 / Details: Rh coated flat mirror, toroidal focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.55→33.87 Å / Num. obs: 20457 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.164 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.55-1.610.9911.5611638189987.2
1.61-1.670.7033.5326823192699.8
1.67-1.750.4125.82324632113100
1.75-1.840.2668.0230372197699.5
1.84-1.950.17412.330235198299.8
1.95-2.10.10819.22311392039100
2.1-2.310.08227.6831729207399.9
2.31-2.650.05641.05324722122100
2.65-3.330.03957.65317902104100
3.330.03467.2831513222398.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.72 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.87 Å
Translation2.5 Å33.87 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→33.87 Å / Cor.coef. Fo:Fc: 0.9484 / Cor.coef. Fo:Fc free: 0.9328 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). DIFFERENCE ELECTRON DENSITY, MOST LIKELY CORRESPONDING TO PROTEIN RESIDUES AT THE N-TERMINAL END OF CHAINS A OR B COULD NOT BE DEFINITIVELY ASSIGNED AND WERE NOT MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1044 5.12 %RANDOM
Rwork0.2162 ---
obs0.2177 20401 --
Displacement parametersBiso max: 128.22 Å2 / Biso mean: 50.0113 Å2 / Biso min: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.7182 Å20 Å20 Å2
2---7.3691 Å20 Å2
3---8.0873 Å2
Refinement stepCycle: LAST / Resolution: 1.55→33.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms978 0 8 84 1070
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d487SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes24HARMONIC2
X-RAY DIFFRACTIONt_gen_planes157HARMONIC5
X-RAY DIFFRACTIONt_it1040HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion134SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1193SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1040HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1405HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion2.32
LS refinement shellResolution: 1.55→1.63 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.245 136 5.06 %
Rwork0.2321 2554 -
all0.2328 2690 -
Refinement TLS params.

L33: 8.3155 °2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°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)
11.983-0.59691.67551.8392-1.1825-0.0843-0.0929-0.11-0.11890.03480.03360.5442-0.54420.04950.207-0.04890.0186-0.1055-0.0155-0.23766.2837-3.00949.17
21.1692-1.49721.90822.2263-2.0125-0.15370.13780.23410.1457-0.2368-0.1968-0.4960.20910.39050.1680.0305-0.0348-0.13260.0115-0.161612.12125.2435.9129
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|42 - 104}A42 - 201
2X-RAY DIFFRACTION2{B|43 - 106}B43 - 201

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