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- PDB-2hes: Cytosolic Iron-sulphur Assembly Protein- 1 -

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Basic information

Entry
Database: PDB / ID: 2hes
TitleCytosolic Iron-sulphur Assembly Protein- 1
ComponentsYdr267cp
KeywordsBIOSYNTHETIC PROTEIN / Beta-propeller / WD40 repeat
Function / homology
Function and homology information


: / cytosolic [4Fe-4S] assembly targeting complex / protein maturation by iron-sulfur cluster transfer / tRNA wobble uridine modification / iron-sulfur cluster assembly / nucleus / cytosol / cytoplasm
Similarity search - Function
Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats ...Probable cytosolic iron-sulfur protein assembly protein, CIAO1/Cia1 / : / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Cytosolic iron-sulfur protein assembly protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSrinivasan, V. / Michel, H. / Lill, R. / Daili, J.A.N. / Pierik, A.J.
CitationJournal: Structure / Year: 2007
Title: Structure of the Yeast WD40 Domain Protein Cia1, a Component Acting Late in Iron-Sulfur Protein Biogenesis.
Authors: Srinivasan, V. / Netz, D.J. / Webert, H. / Mascarenhas, J. / Pierik, A.J. / Michel, H. / Lill, R.
History
DepositionJun 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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_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_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_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
X: Ydr267cp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3562
Polymers37,3151
Non-polymers401
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.211, 70.026, 130.366
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 Ydr267cp


Mass: 37315.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YDR267cp / Production host: Escherichia coli (E. coli) / References: UniProt: Q05583
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22%PEG 4000, 20mM tris-HCl, pH = 8.0 and 100mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.931
SYNCHROTRONEMBL/DESY, HAMBURG X3120.976
Detector
TypeIDDetector
MARRESEARCH1CCD
MAR scanner 345 mm plate2IMAGE PLATE
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9311
20.9761
ReflectionResolution: 1.7→17.98 Å / Num. obs: 34661 / % possible obs: 98.34 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.7→1.744 Å / % possible all: 98.34

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→17.98 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.786 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27544 1115 3.1 %RANDOM
Rwork0.22424 ---
obs0.22584 34661 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.7→17.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 1 301 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222496
X-RAY DIFFRACTIONr_angle_refined_deg1.7841.9143394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9495304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62124.609115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.66615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.164159
X-RAY DIFFRACTIONr_chiral_restr0.120.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021879
X-RAY DIFFRACTIONr_nbd_refined0.310.21291
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2313
X-RAY DIFFRACTIONr_metal_ion_refined0.1670.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.233
X-RAY DIFFRACTIONr_mcbond_it1.0991.51556
X-RAY DIFFRACTIONr_mcangle_it1.80422435
X-RAY DIFFRACTIONr_scbond_it2.631136
X-RAY DIFFRACTIONr_scangle_it3.6394.5959
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 55 -
Rwork0.27 2271 -
obs-2326 88.04 %
Refinement TLS params.Method: refined / Origin x: 16.379 Å / Origin y: 6.963 Å / Origin z: 17.836 Å
111213212223313233
T-0.1755 Å2-0.0315 Å2-0.0292 Å2--0.1331 Å20.0258 Å2---0.1415 Å2
L1.2105 °20.1023 °20.5075 °2-1.9323 °2-0.0465 °2--2.4514 °2
S0.1259 Å °-0.2274 Å °-0.1445 Å °0.1915 Å °0.0012 Å °-0.0981 Å °0.266 Å °-0.0735 Å °-0.127 Å °
Refinement TLS groupSelection: ALL

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