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- PDB-2d2a: Crystal Structure of Escherichia coli SufA Involved in Biosynthes... -

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Basic information

Entry
Database: PDB / ID: 2d2a
TitleCrystal Structure of Escherichia coli SufA Involved in Biosynthesis of Iron-sulfur Clusters
ComponentsSufA protein
KeywordsMETAL TRANSPORT / Iron-sulfur cluster / iron / SUF / SufA / IscA / YadR
Function / homology
Function and homology information


protein maturation by iron-sulfur cluster transfer / iron-sulfur cluster assembly / 2 iron, 2 sulfur cluster binding / response to oxidative stress / structural molecule activity / cytosol / cytoplasm
Similarity search - Function
FeS assembly scaffold SufA / FeS cluster insertion, C-terminal, conserved site / Hypothetical hesB/yadR/yfhF family signature. / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWada, K. / Hasegawa, Y. / Gong, Z. / Minami, Y. / Fukuyama, K. / Takahashi, Y.
CitationJournal: Febs Lett. / Year: 2005
Title: Crystal structure of Escherichia coli SufA involved in biosynthesis of iron-sulfur clusters: Implications for a functional dimer
Authors: Wada, K. / Hasegawa, Y. / Gong, Z. / Minami, Y. / Fukuyama, K. / Takahashi, Y.
History
DepositionSep 5, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SufA protein
B: SufA protein


Theoretical massNumber of molelcules
Total (without water)32,1542
Polymers32,1542
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9 kcal/mol
Surface area12640 Å2
MethodPISA
2
A: SufA protein

B: SufA protein


Theoretical massNumber of molelcules
Total (without water)32,1542
Polymers32,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_745-x+2,y-1/2,-z+1/21
Buried area1930 Å2
ΔGint-14 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.162, 88.500, 122.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein SufA protein


Mass: 16076.958 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P77667
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.1 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG2000MME, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 29, 2004
RadiationMonochromator: SI(111) DOUBLE MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8136 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 40.1 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.349 / Num. unique all: 808 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S98

1s98


Resolution: 2.7→41.6 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 421277.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 817 10.6 %RANDOM
Rwork0.232 ---
all0.237 7692 --
obs0.232 7692 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.8321 Å2 / ksol: 0.370499 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.42 Å20 Å20 Å2
2--5.78 Å20 Å2
3----2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 37 1677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.047
X-RAY DIFFRACTIONc_angle_deg3.4
X-RAY DIFFRACTIONc_dihedral_angle_d28.6
X-RAY DIFFRACTIONc_improper_angle_d3.05
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 125 10.9 %
Rwork0.26 1021 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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