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- PDB-1mzg: X-Ray Structure of SufE from E.coli Northeast Structural Genomics... -

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Basic information

Entry
Database: PDB / ID: 1mzg
TitleX-Ray Structure of SufE from E.coli Northeast Structural Genomics (NESG) Consortium Target ER30
ComponentsSufE ProteinShanghai University of Finance and Economics
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


sulfur incorporation into metallo-sulfur cluster / sulfur carrier activity / iron-sulfur cluster assembly / positive regulation of catalytic activity / enzyme activator activity / response to oxidative stress / cytoplasm
Similarity search - Function
Cysteine desulfuration protein SufE / Fe-S metabolism associated domain, SufE-like / Fe-S metabolism associated domain / Sufe protein. Chain: A - #10 / Sufe protein. Chain: A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cysteine desulfuration protein SufE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKuzin, A. / Edstrom, W.C. / Xiao, R. / Acton, T.B. / Rost, B. / Tong, L. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Mol.Biol. / Year: 2004
Title: The SufE sulfur-acceptor protein contains a conserved core structure that mediates interdomain interactions in a variety of redox protein complexes
Authors: Goldsmith-Fischman, S. / Kuzin, A. / Edstrom, W.C. / Benach, J. / Shastry, R. / Xiao, R. / Acton, T.B. / Honig, B. / Montelione, G.T. / Hunt, J.F.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SufE Protein
B: SufE Protein


Theoretical massNumber of molelcules
Total (without water)34,2462
Polymers34,2462
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.190, 54.401, 120.685
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 SufE Protein / Shanghai University of Finance and Economics


Mass: 17122.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: HYPOTHETICAL TARGET ER30 / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P76194
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.02 Å3/Da / Density % sol: 39.17 %
Crystal growTemperature: 302 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: 34% PEG3350, 3% Methanol, 0.1M Tris pH 8.9, 0.2M Sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 302.0K
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
134 %(w/v)PEG33501reservoir
2200 mMsodium acetate1reservoir
33 %(v/v)methanol1reservoir
4100 mMTris-HCl1reservoirpH8.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9792
DetectorDate: Aug 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→27.2 Å / Num. obs: 17893 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.3 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 19.9 Å / % possible obs: 98.6 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 89.3 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→19.91 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1252026.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.251 862 4.8 %RANDOM
Rwork0.208 ---
all-17893 --
obs-17882 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9236 Å2 / ksol: 0.350805 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-9.22 Å20 Å20 Å2
2--1.03 Å20 Å2
3----10.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 0 185 2515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_d21.5
X-RAY DIFFRACTIONo_improper_angle_d0.91
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 130 4.9 %
Rwork0.226 2499 -
obs--82.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 19.9 Å / % reflection Rfree: 4.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg21.5
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg0.91

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