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- PDB-3lpq: Human MitoNEET with 2Fe-2S Coordinating Ligand His 87 Replaced Wi... -

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Basic information

Entry
Database: PDB / ID: 3lpq
TitleHuman MitoNEET with 2Fe-2S Coordinating Ligand His 87 Replaced With Cys
ComponentsCDGSH iron sulfur domain-containing protein 1
KeywordsMETAL BINDING PROTEIN / CDGSH protein fold / 2Fe-2S cluster / NEET fold / homodimer / Iron / Iron-sulfur / Membrane / Metal-binding / Mitochondrion / Mitochondrion outer membrane / Signal-anchor / Transmembrane
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: 1.7 Å
AuthorsConlan, A.R. / Homer, C. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Zuris, J. / Nechushtai, R. / Paddock, M.L. / Jennings, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Mutation of the His ligand in mitoNEET stabilizes the 2Fe-2S cluster despite conformational heterogeneity in the ligand environment.
Authors: Conlan, A.R. / Paddock, M.L. / Homer, C. / Axelrod, H.L. / Cohen, A.E. / Abresch, E.C. / Zuris, J.A. / Nechushtai, R. / Jennings, P.A.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Feb 21, 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_alt_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.pdbx_ptnr1_label_alt_id / _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 1
B: CDGSH iron sulfur domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8034
Polymers18,4512
Non-polymers3522
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-54 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.311, 49.587, 59.222
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 1 / MitoNEET


Mass: 9225.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3) / Gene: C10orf70, CISD1, MDS029, ZCD1 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus RIL(DE3) / References: UniProt: Q9NZ45
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 1.99 Å3/Da / Density % sol: 38.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 17% PEG 3000, 100 mM Tris-Hcl pH 8.0, 150 mM NaCl, vapor diffusion, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-110.9795
SYNCHROTRONSSRL BL9-220.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 15, 2007
MARmosaic 3252CCDNov 15, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→38.019 Å / Num. obs: 16489 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.7970.7261.11644223560.72699.8
1.79-1.97.10.4341.81582822410.43499.7
1.9-2.037.10.2523.11482120970.25299.7
2.03-2.1970.1544.91383319740.15499.8
2.19-2.470.1067.11278818270.10699.9
2.4-2.6970.07110.11163516620.07199.8
2.69-3.16.90.05312.31022014780.05399.8
3.1-3.86.70.03615.5856012700.03699.7
3.8-5.386.50.03316.564949970.03399.8
5.38-38.026.10.03217.735785870.03298.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.92 Å38.02 Å
Translation1.92 Å38.02 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.89 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.221 / WRfactor Rwork: 0.174 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.849 / SU B: 4.045 / SU ML: 0.078 / SU R Cruickshank DPI: 0.112 / SU Rfree: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLS MOTION DETERMINATION SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 835 5.1 %RANDOM
Rwork0.178 ---
obs0.18 16487 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 48.16 Å2 / Biso mean: 21.526 Å2 / Biso min: 5.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å20 Å20 Å2
2---0.49 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 8 101 1280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221282
X-RAY DIFFRACTIONr_bond_other_d0.0010.02889
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9441733
X-RAY DIFFRACTIONr_angle_other_deg0.8832178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2725168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.91524.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.56815231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.89157
X-RAY DIFFRACTIONr_chiral_restr0.0880.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021441
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_mcbond_it1.3643787
X-RAY DIFFRACTIONr_mcbond_other0.493315
X-RAY DIFFRACTIONr_mcangle_it2.14951264
X-RAY DIFFRACTIONr_scbond_it3.5248495
X-RAY DIFFRACTIONr_scangle_it5.09311456
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 66 -
Rwork0.248 1119 -
all-1185 -
obs--99.41 %
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)
12.8318-0.1962.12959.9491-12.525917.03570.45060.6263-0.6738-0.14420.26910.24350.48840.1446-0.71970.72250.2793-0.110.3354-0.08060.3277-9.818558.7347-11.2104
21.45720.3664-0.4991.71130.16913.3488-0.04170.0508-0.0542-0.0729-0.0146-0.07150.1710.07180.05630.10560.02210.00020.06930.01490.117611.375445.36377.8139
311.52954.92044.05363.33852.01651.4916-0.47241.43720.29360.07560.17740.9726-0.09440.40410.2950.91090.14960.04790.5968-0.16910.7373-17.504239.33517.2787
40.8781-0.4406-0.71311.50820.34353.40390.02090.00510.11280.0083-0.0195-0.1034-0.16060.0937-0.00140.10140.00130.00540.07650.0150.124411.308554.63835.3549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 39
2X-RAY DIFFRACTION2A40 - 107
3X-RAY DIFFRACTION3B34 - 41
4X-RAY DIFFRACTION4B42 - 107

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