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- PDB-2clb: The structure of the DPS-like protein from Sulfolobus solfataricu... -

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Basic information

Entry
Database: PDB / ID: 2clb
TitleThe structure of the DPS-like protein from Sulfolobus solfataricus reveals a bacterioferritin-like di-metal binding site within a Dps- like dodecameric assembly
ComponentsDPS-LIKE PROTEIN
KeywordsMETAL BINDING PROTEIN / DI-IRON CARBOXYLATE / HYPOTHETICAL PROTEIN / BACTERIOFERRITIN / HYDROGEN PEROXIDE / DPS / ARCHAEA / DPS- LIKE / OXIDATIVE STRESS
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / nucleoid / intracellular sequestering of iron ion / ferroxidase activity / ferric iron binding / iron ion binding / heme binding / cytosol
Similarity search - Function
DPS-like protein, ferritin-like diiron-binding domain / DNA-binding protein from starved cells-like / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA protection during starvation protein
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsGauss, G.H. / Benas, P. / Wiedenheft, B. / Young, M. / Douglas, T. / Lawrence, C.M.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of the Dps-Like Protein from Sulfolobus Solfataricus Reveals a Bacterioferritin-Like Dimetal Binding Site within a Dps-Like Dodecameric Assembly.
Authors: Gauss, G.H. / Benas, P. / Wiedenheft, B. / Young, M. / Douglas, T. / Lawrence, C.M.
History
DepositionApr 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DPS-LIKE PROTEIN
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
M: DPS-LIKE PROTEIN
N: DPS-LIKE PROTEIN
O: DPS-LIKE PROTEIN
P: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,25324
Polymers176,2838
Non-polymers97016
Water2,180121
1
A: DPS-LIKE PROTEIN
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
hetero molecules

A: DPS-LIKE PROTEIN
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
hetero molecules

A: DPS-LIKE PROTEIN
B: DPS-LIKE PROTEIN
C: DPS-LIKE PROTEIN
D: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,88036
Polymers264,42512
Non-polymers1,45524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_656-z+1,x+1/2,-y+3/21
crystal symmetry operation11_466y-1/2,-z+3/2,-x+11
MethodPQS
2
M: DPS-LIKE PROTEIN
N: DPS-LIKE PROTEIN
O: DPS-LIKE PROTEIN
P: DPS-LIKE PROTEIN
hetero molecules

M: DPS-LIKE PROTEIN
N: DPS-LIKE PROTEIN
O: DPS-LIKE PROTEIN
P: DPS-LIKE PROTEIN
hetero molecules

M: DPS-LIKE PROTEIN
N: DPS-LIKE PROTEIN
O: DPS-LIKE PROTEIN
P: DPS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,88036
Polymers264,42512
Non-polymers1,45524
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation5_555z,x,y1
MethodPQS
Unit cell
Length a, b, c (Å)212.928, 212.928, 212.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.42017, -0.45935, 0.7826), (-0.21237, 0.88824, 0.40733), (-0.88224, 0.00495, -0.47077)25.15704, -35.22717, 280.72784
2given(0.88651, -0.41435, 0.20597), (-0.01195, -0.46548, -0.88498), (0.46256, 0.78207, -0.41761)39.71066, 376.47821, 75.71466
3given(0.88244, -0.01272, 0.47026), (-0.42163, -0.46476, 0.77861), (0.20865, -0.88535, -0.41548)-66.47775, 133.43034, 355.83487
4given(-0.45927, -0.42022, -0.78262), (0.88829, -0.21248, -0.40719), (0.00482, -0.88219, 0.47086)231.34637, 131.76146, 202.64969
5given(-0.41452, 0.88664, -0.20505), (-0.465, -0.01267, 0.88522), (0.78227, 0.46229, 0.41754)25.19823, 116.82986, -18.39075
6given(-0.01304, 0.88224, -0.47061), (-0.46474, -0.42207, -0.77838), (-0.88535, 0.20857, 0.41552)11.13016, 338.38898, 187.0293
7given(0.00054, 1, -0.00022), (1, -0.00054, -0.00048), (-0.00048, -0.00021, -1)-53.25972, 53.36218, 266.22922

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Components

#1: Protein
DPS-LIKE PROTEIN


Mass: 22035.432 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE PROTEIN / Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P95855
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.4 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.5
Details: 0.5 M LICL 9 % PEG 6000 0.01 CACL2 0.05 TRIS-CL PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.28237
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28237 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 56599 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 7.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.7 / % possible all: 61

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.093 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.554 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2891 5.1 %RANDOM
Rwork0.199 ---
obs0.2 53568 90.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10963 0 16 121 11100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211179
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210322
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.98515091
X-RAY DIFFRACTIONr_angle_other_deg0.737324044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.61351339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53824.212539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.584152102
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7961580
X-RAY DIFFRACTIONr_chiral_restr0.0460.21651
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212224
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022204
X-RAY DIFFRACTIONr_nbd_refined0.1970.22699
X-RAY DIFFRACTIONr_nbd_other0.1660.29825
X-RAY DIFFRACTIONr_nbtor_refined0.1710.25462
X-RAY DIFFRACTIONr_nbtor_other0.080.25804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.243
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.2320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.96638780
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.088410751
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93665268
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7994340
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 140
Rwork0.26 2591
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.55091.2542-0.7373.1063-0.42481.73670.0424-0.2714-0.09160.2807-0.1281-0.0072-0.0718-0.06040.08570.2260.0463-0.03590.06840.07570.052758.4491148.4056189.4072
24.04210.6377-0.10051.30010.08032.1712-0.0650.0595-0.39350.0153-0.0236-0.32170.10720.00310.08860.12410.0932-0.07010.040.07120.232469.3507134.281171.634
34.1843-0.8799-0.61742.1431-0.18841.86950.1025-0.2837-0.12130.3071-0.0994-0.0445-0.09070.1043-0.00310.2212-0.1114-0.16620.040.00950.019973.2163175.6332180.3127
43.0258-0.62591.42522.1285-0.7112.7582-0.06510.0704-0.10250.0246-0.0562-0.3076-0.11710.10040.1213-0.02580.01240.0438-0.0032-0.08380.157780.8097161.2897140.959
52.94291.14450.33173.26860.78661.7483-0.10540.2970.0299-0.21520.03630.10720.05170.04670.06910.070.0641-0.06710.22990.03570.055495.1486111.657976.7619
61.24320.634-0.09464.1216-0.20422.3134-0.02190.02530.30450.0671-0.06120.37460.0141-0.1040.08310.04120.1078-0.06660.1270.0620.220980.913122.400594.4953
72.0185-0.88540.21914.21870.73211.9064-0.08650.32170.0395-0.27740.12150.1038-0.11410.094-0.0350.0359-0.1174-0.01210.22220.16570.0245122.3736126.439685.8752
82.1588-0.72560.68063.1544-1.41582.7499-0.080.00110.30360.0793-0.03630.0758-0.11170.09590.1162-0.01690.01020.0842-0.0316-0.03910.165108.046134.0364125.2127
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 174
2X-RAY DIFFRACTION2B8 - 174
3X-RAY DIFFRACTION3C6 - 174
4X-RAY DIFFRACTION4D7 - 174
5X-RAY DIFFRACTION5M6 - 174
6X-RAY DIFFRACTION6N7 - 174
7X-RAY DIFFRACTION7O6 - 174
8X-RAY DIFFRACTION8P7 - 174

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