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- PDB-1x0g: Crystal Structure of IscA with the [2Fe-2S] cluster -

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Basic information

Entry
Database: PDB / ID: 1x0g
TitleCrystal Structure of IscA with the [2Fe-2S] cluster
ComponentsIscA
KeywordsMETAL BINDING PROTEIN / [2Fe-2S] / biosynthesis / cyanobacteria / domain swapping / Fe-S cluster / iron / iron-sulfur cluster protein / Isc / IscA / scaffold / sulfur / tetrameric / three conserved Cys
Function / homology
Function and homology information


: / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
: / FeS cluster insertion protein / Hypothetical Protein Aq_1857; Chain: A; / HesB-like domain / FeS cluster biogenesis / HesB-like domain superfamily / Iron-sulphur cluster biosynthesis / Sandwich / Mainly Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Tll0464 protein
Similarity search - Component
Biological speciesThermosynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMorimoto, K. / Yamashita, E. / Kondou, Y. / Lee, S.J. / Tsukihara, T. / Nakai, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Asymmetric IscA Homodimer with an Exposed [2Fe-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold.
Authors: Morimoto, K. / Yamashita, E. / Kondou, Y. / Lee, S.J. / Arisaka, F. / Tsukihara, T. / Nakai, M.
History
DepositionMar 22, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: IscA
B: IscA
C: IscA
D: IscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8708
Polymers49,4724
Non-polymers3984
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15580 Å2
ΔGint-146 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.472, 102.788, 137.032
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-120-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14A
24C
15B
25D
16B
26D
17B
27D
18B
28D
19A
29C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLUGLU4AA2 - 112 - 11
21VALVALGLUGLU4CC2 - 112 - 11
12ILEILEVALVAL5AA27 - 4727 - 47
22ILEILEVALVAL5CC27 - 4727 - 47
13GLYGLYILEILE1AA76 - 8276 - 82
23GLYGLYILEILE1CC76 - 8276 - 82
14ALAALAARGARG1AA89 - 11189 - 111
24ALAALAARGARG1CC89 - 11189 - 111
15VALVALLEULEU4BB2 - 152 - 15
25VALVALLEULEU4DD2 - 152 - 15
16ALAALASERSER4BB26 - 3526 - 35
26ALAALASERSER4DD26 - 3526 - 35
17ASPASPALAALA1BB39 - 6739 - 67
27ASPASPALAALA1DD39 - 6739 - 67
18GLNGLNCYSCYS4BB99 - 10399 - 103
28GLNGLNCYSCYS4DD99 - 10399 - 103
19ALAALAALAALA1AA48 - 6848 - 68
29ALAALAALAALA1CC48 - 6848 - 68

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein
IscA / hypothetical protein tll0464


Mass: 12368.081 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermosynechococcus elongatus (bacteria)
Strain: BP-1 / Gene: tll0464 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)RIL / References: UniProt: Q8DLM0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 36 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 2.5M NaCl, 0.1M Potassium phosphate pH6.2, 5MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.9
Detector
TypeIDDetectorDate
Bruker DIP-60401CCDJul 7, 2004
DIP60402IMAGE PLATESep 23, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→80 Å / Num. obs: 19261 / % possible obs: 96 % / Redundancy: 12.5 % / Biso Wilson estimate: 59.41 Å2 / Rsym value: 0.071 / Net I/σ(I): 39.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.311 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.945 / SU B: 19.559 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.436 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2415 932 4.9 %RANDOM
Rwork0.20107 ---
obs0.20302 18065 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.352 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---1.48 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 10 36 3348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0223370
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5031.9654567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.9835421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48323.522159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.19215559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.61534
X-RAY DIFFRACTIONr_chiral_restr0.140.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2760.21556
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.340.22297
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1830.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.271
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1411.52121
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.17123385
X-RAY DIFFRACTIONr_scbond_it3.4231289
X-RAY DIFFRACTIONr_scangle_it5.6334.51178
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
3A58tight positional0.10.05
4A178tight positional0.160.05
7B231tight positional0.10.05
9A155tight positional0.050.05
1A74medium positional0.380.5
2A84medium positional0.120.5
5B110medium positional0.340.5
6B78medium positional0.270.5
8B32medium positional0.380.5
2A89loose positional0.35
3A58tight thermal0.160.5
4A178tight thermal0.410.5
7B231tight thermal0.330.5
9A155tight thermal0.310.5
1A74medium thermal0.522
2A84medium thermal1.482
5B110medium thermal1.032
6B78medium thermal1.652
8B32medium thermal3.052
2A89loose thermal3.0610
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 71 -
Rwork0.281 1272 -
obs--95.86 %

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