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- PDB-6a6f: Crystal structure of Putative iron-sulfur cluster assembly scaffo... -

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Basic information

Entry
Database: PDB / ID: 6a6f
TitleCrystal structure of Putative iron-sulfur cluster assembly scaffold protein for SUF system (FiSufU) from thermophilic Fervidobacterium Islandicum AW-1
ComponentsIron-sulfur cluster assembly scaffold protein NifU
KeywordsBIOSYNTHETIC PROTEIN / SufE / Thermophile / Fe-S cluster scaffold protein
Function / homology
Function and homology information


iron-sulfur cluster assembly / iron-sulfur cluster binding / iron ion binding
Similarity search - Function
Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / NIF system FeS cluster assembly, NifU, N-terminal / NifU-like N terminal domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / SUF system NifU family Fe-S cluster assembly protein
Similarity search - Component
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDhanasingh, I. / Jin, H.S. / Lee, D.W. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
2014R1A2A2A01006765 Korea, Republic Of
2009-0064846 Korea, Republic Of
CitationJournal: Microb Biotechnol / Year: 2020
Title: The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation.
Authors: Jin, H.S. / Dhanasingh, I. / Sung, J.Y. / La, J.W. / Lee, Y. / Lee, E.M. / Kang, Y. / Lee, D.Y. / Lee, S.H. / Lee, D.W.
History
DepositionJun 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._citation.title / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-sulfur cluster assembly scaffold protein NifU
B: Iron-sulfur cluster assembly scaffold protein NifU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,18520
Polymers31,7112
Non-polymers1,47418
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-62 kcal/mol
Surface area13920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.873, 30.665, 77.955
Angle α, β, γ (deg.)90.00, 98.65, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iron-sulfur cluster assembly scaffold protein NifU / FiSufE


Mass: 15855.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08310 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1B0VLW5

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Non-polymers , 5 types, 261 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.01M Nickel Chloride, PEG MEM 2000, 0.1M Tris HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 18186 / % possible obs: 98.74 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.0471 / Net I/σ(I): 24.96
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.092

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QQ4

2qq4


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.632 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22637 919 5.1 %RANDOM
Rwork0.16296 ---
obs0.16615 17273 98.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å20.08 Å2
2---0.12 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 73 243 2496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192277
X-RAY DIFFRACTIONr_bond_other_d0.0010.022179
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9813024
X-RAY DIFFRACTIONr_angle_other_deg0.81935095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4515270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20626100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39115442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.183152
X-RAY DIFFRACTIONr_chiral_restr0.1030.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022414
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1342.5191086
X-RAY DIFFRACTIONr_mcbond_other2.1322.5171085
X-RAY DIFFRACTIONr_mcangle_it3.1393.7641354
X-RAY DIFFRACTIONr_mcangle_other3.1383.7671355
X-RAY DIFFRACTIONr_scbond_it3.3643.1171191
X-RAY DIFFRACTIONr_scbond_other3.3643.1171191
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4154.3871671
X-RAY DIFFRACTIONr_long_range_B_refined7.432.1372671
X-RAY DIFFRACTIONr_long_range_B_other7.39832.1632672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.092→2.146 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 52 -
Rwork0.198 1079 -
obs--85.23 %

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