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- PDB-1vh4: Crystal structure of a stabilizer of iron transporter -

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Basic information

Entry
Database: PDB / ID: 1vh4
TitleCrystal structure of a stabilizer of iron transporter
ComponentsSufD protein
KeywordsPROTEIN BINDING PROTEIN / structural genomics
Function / homologySUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / response to oxidative stress / Iron-sulfur cluster assembly protein SufD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Se-Met MAD phasing / Resolution: 1.75 Å
AuthorsStructural GenomiX
CitationJournal: Proteins / Year: 2005
Title: Structural analysis of a set of proteins resulting from a bacterial genomics project
Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J.
History
DepositionDec 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SufD protein
B: SufD protein


Theoretical massNumber of molelcules
Total (without water)96,4882
Polymers96,4882
Non-polymers00
Water8,935496
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.996, 96.154, 90.808
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SufD protein


Mass: 48244.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: SUFD, B1681 / Production host: Escherichia coli (E. coli) / References: UniProt: P77689
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 496 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMHEPES1droppH7.5
2150 mM1dropNaCl
310 mMmethionine1drop
410 %glycerol1drop
55 mMdithiothreitol1drop
610 mg/mlprotein1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.9794, 0.9794
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→48.08 Å / Num. all: 93194 / Num. obs: 93194 / % possible obs: 97.9 % / Redundancy: 5.55 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 29.2
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5.3 / % possible all: 95
Reflection
*PLUS
Redundancy: 5.6 %
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementMethod to determine structure: Se-Met MAD phasing / Resolution: 1.75→48.08 Å / σ(F): 0
RfactorNum. reflection
Rfree0.238 4667
Rwork0.212 -
obs-93194
Solvent computationSolvent model: Babinet bulk solvent correction / Bsol: 365.275 Å2 / ksol: 0.995 e/Å3
Displacement parametersBiso mean: 23.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.574 Å20 Å20.174 Å2
2--0.558 Å20 Å2
3---0.111 Å2
Refine Biso Class: all / Treatment: isotropic
Refinement stepCycle: LAST / Resolution: 1.75→48.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6446 0 0 496 6942
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d1.602
X-RAY DIFFRACTIONp_planar_tor3.372
X-RAY DIFFRACTIONp_chiral_restr0.104
X-RAY DIFFRACTIONp_plane_restr0.009
X-RAY DIFFRACTIONp_mcbond_it1.123
X-RAY DIFFRACTIONp_mcangle_it2.016
X-RAY DIFFRACTIONp_scbond_it1.955
X-RAY DIFFRACTIONp_scangle_it3.152
Software
*PLUS
Version: 4 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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