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- PDB-1zs3: The crystal structure of the Lactococcus lactis MG1363 DpsB protein -

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Basic information

Entry
Database: PDB / ID: 1zs3
TitleThe crystal structure of the Lactococcus lactis MG1363 DpsB protein
ComponentsLactococcus lactis MG1363 DpsA
KeywordsDNA BINDING PROTEIN / Oxidative stress / Dps / DNA binding / Lactic acid bacteria
Function / homologyFerritin, core subunit, four-helix bundle / Ferritin / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsStillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. ...Stillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. / Artymiuk, P.J. / Green, J.
Citation
Journal: Mol.Microbiol. / Year: 2005
Title: The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N-terminal helix that is required for DNA binding.
Authors: Stillman, T.J. / Upadhyay, M. / Norte, V.A. / Sedelnikova, S.E. / Carradus, M. / Tzokov, S. / Bullough, P.A. / Shearman, C.A. / Gasson, M.J. / Williams, C.H. / Artymiuk, P.J. / Green, J.
#1: Journal: Mol.Microbiol. / Year: 1999
Title: Two operons that encode FNR-like proteins in Lactococcus lactis
Authors: Gostick, D.O. / Griffin, H.G. / Shearman, C.A. / Scott, C. / Green, J. / Gasson, M.J. / Guest, J.R.
History
DepositionMay 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 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.name
Revision 1.4Aug 23, 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: Lactococcus lactis MG1363 DpsA
B: Lactococcus lactis MG1363 DpsA
C: Lactococcus lactis MG1363 DpsA
D: Lactococcus lactis MG1363 DpsA
E: Lactococcus lactis MG1363 DpsA
F: Lactococcus lactis MG1363 DpsA
G: Lactococcus lactis MG1363 DpsA
H: Lactococcus lactis MG1363 DpsA
I: Lactococcus lactis MG1363 DpsA
J: Lactococcus lactis MG1363 DpsA
K: Lactococcus lactis MG1363 DpsA
L: Lactococcus lactis MG1363 DpsA


Theoretical massNumber of molelcules
Total (without water)252,14112
Polymers252,14112
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36800 Å2
ΔGint-221 kcal/mol
Surface area82960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.977, 128.379, 193.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe 12 subunits in the asymmetric unit form the biological assembly, a dodecamer with 23 symmetry.

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Components

#1: Protein
Lactococcus lactis MG1363 DpsA


Mass: 21011.783 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Gene: flpB / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 57.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 2.0M Sodium Formate, 0.1M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX14.210.98
SYNCHROTRONSRS PX14.220.98
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDMay 11, 2001Mirrors
ADSC QUANTUM 42CCDJun 29, 2001Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→15 Å / Num. all: 85912 / Num. obs: 85912 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 7.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.7 / Num. unique all: 12388 / Rsym value: 0.407 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1qgh

1qgh


Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.166 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.755 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25779 4108 5.1 %RANDOM
Rwork0.20683 ---
all0.2094 77125 --
obs0.20941 77125 92.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16644 0 0 131 16775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02216968
X-RAY DIFFRACTIONr_bond_other_d0.0430.0215444
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.96322884
X-RAY DIFFRACTIONr_angle_other_deg1.59336084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71552040
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0980.22556
X-RAY DIFFRACTIONr_gen_planes_refined0.0250.0218612
X-RAY DIFFRACTIONr_gen_planes_other0.050.023372
X-RAY DIFFRACTIONr_nbd_refined0.2340.24167
X-RAY DIFFRACTIONr_nbd_other0.2370.217303
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0970.211003
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.882210212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.662.516440
X-RAY DIFFRACTIONr_scbond_it1.90636756
X-RAY DIFFRACTIONr_scangle_it3.3784.56444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.326 280
Rwork0.285 5043

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