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- PDB-1zuj: The crystal structure of the Lactococcus lactis MG1363 DpsA protein -

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Basic information

Entry
Database: PDB / ID: 1zuj
TitleThe crystal structure of the Lactococcus lactis MG1363 DpsA protein
Componentshypothetical protein Llacc01001955
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: 2.9 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 31, 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: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_special_symmetry
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: hypothetical protein Llacc01001955
B: hypothetical protein Llacc01001955
C: hypothetical protein Llacc01001955
D: hypothetical protein Llacc01001955


Theoretical massNumber of molelcules
Total (without water)83,8074
Polymers83,8074
Non-polymers00
Water81145
1
A: hypothetical protein Llacc01001955
B: hypothetical protein Llacc01001955
C: hypothetical protein Llacc01001955
D: hypothetical protein Llacc01001955

A: hypothetical protein Llacc01001955
B: hypothetical protein Llacc01001955
C: hypothetical protein Llacc01001955
D: hypothetical protein Llacc01001955

A: hypothetical protein Llacc01001955
B: hypothetical protein Llacc01001955
C: hypothetical protein Llacc01001955
D: hypothetical protein Llacc01001955


Theoretical massNumber of molelcules
Total (without water)251,42012
Polymers251,42012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area38500 Å2
ΔGint-180 kcal/mol
Surface area79310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)131.840, 131.840, 325.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11D-188-

HOH

DetailsThe biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operations: 2-y, x-y, z and 2-x+y, 2-x, z.

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Components

#1: Protein
hypothetical protein Llacc01001955


Mass: 20951.639 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: MG1363 / Gene: flpA / 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.: 45 / 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: 3.26 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7M ammonium sulphate, 0.1M HEPES/Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX14.111.488
SYNCHROTRONSRS PX14.121.488
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDDec 5, 2001Mirrors
ADSC QUANTUM 42CCDDec 5, 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: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. all: 22949 / Num. obs: 22949 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 77.4 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3298 / Rsym value: 0.382 / % possible all: 93.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZS3

1zs3


Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.839 / SU B: 21.27 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.524 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32216 1098 5.2 %RANDOM
Rwork0.25256 ---
all0.25622 20210 --
obs0.25622 20210 87.06 %-
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: 53.953 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20.67 Å20 Å2
2--1.35 Å20 Å2
3----2.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 0 45 5589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225668
X-RAY DIFFRACTIONr_bond_other_d0.0020.025040
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9547636
X-RAY DIFFRACTIONr_angle_other_deg0.933311812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.1145668
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_restr0.0960.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026232
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021152
X-RAY DIFFRACTIONr_nbd_refined0.2530.21644
X-RAY DIFFRACTIONr_nbd_other0.2310.26294
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.23524
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5041.53344
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97325376
X-RAY DIFFRACTIONr_scbond_it1.22432324
X-RAY DIFFRACTIONr_scangle_it2.1734.52260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.457 72
Rwork0.326 1270

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