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- PDB-2zu0: Crystal structure of SufC-SufD complex involved in the iron-sulfu... -

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Basic information

Entry
Database: PDB / ID: 2zu0
TitleCrystal structure of SufC-SufD complex involved in the iron-sulfur cluster biosynthesis
Components
  • Probable ATP-dependent transporter sufC
  • Protein sufD
KeywordsBiosynthetic Protein/Protein Binding / Iron-sulfur cluster / ABC-ATPase / ATP-binding / Cytoplasm / Nucleotide-binding / Transport / Biosynthetic Protein-Protein Binding COMPLEX
Function / homology
Function and homology information


iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / response to radiation / response to oxidative stress / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
Monooxygenase / Monooxygenase - #10 / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / SUF system FeS cluster assembly, SufBD / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. / Helix non-globular ...Monooxygenase / Monooxygenase - #10 / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / SUF system FeS cluster assembly, SufBD / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. / Helix non-globular / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / Special / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable ATP-dependent transporter SufC / Iron-sulfur cluster assembly protein SufD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWada, K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Molecular dynamism of Fe-S cluster biosynthesis implicated by the structure of SufC(2)-SufD(2) complex
Authors: Wada, K. / Sumi, N. / Nagai, R. / Iwasaki, K. / Sato, T. / Suzuki, K. / Hasegawa, Y. / Kitaoka, S. / Minami, Y. / Outten, F.W. / Takahashi, Y. / Fukuyama, K.
History
DepositionOct 11, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Protein sufD
B: Protein sufD
C: Probable ATP-dependent transporter sufC
D: Probable ATP-dependent transporter sufC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2585
Polymers153,0624
Non-polymers1951
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-24 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.110, 106.150, 171.670
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 Protein sufD


Mass: 46884.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: SufC and SufD / Plasmid: pMW219 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P77689
#2: Protein Probable ATP-dependent transporter sufC


Mass: 29646.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: SufC and SufD / Plasmid: pMW219 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P77499
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 5%(w/v) PEG 6000, 0.1M MES (pH 8.0-8.5), EVAPORATION, temperature 293K
PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2007
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 89901 / Num. obs: 89901 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.291 / Num. unique all: 8867 / Rsym value: 0.291 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VH4

1vh4


Resolution: 2.2→45.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 68526.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 8712 10 %RANDOM
Rwork0.234 ---
obs0.234 87226 97.2 %-
all-87226 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.7925 Å2 / ksol: 0.367394 e/Å3
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.67 Å20 Å20 Å2
2--1.11 Å20 Å2
3----4.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8742 0 12 289 9043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 1365 10 %
Rwork0.248 12218 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5PNP.paramPNP.top

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