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- PDB-1tjo: Iron-oxo clusters biomineralizing on protein surfaces. Structural... -

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Basic information

Entry
Database: PDB / ID: 1tjo
TitleIron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states
ComponentsIron-rich dpsA-homolog protein
KeywordsMETAL BINDING PROTEIN / DpsA / ferritin / low-iron
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm
Similarity search - Function
DNA-binding protein Dps / 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 speciesHalobacterium salinarum (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZeth, K. / Offermann, S. / Essen, L.O. / Oesterhelt, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Iron-oxo clusters biomineralizing on protein surfaces: structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.
Authors: Zeth, K. / Offermann, S. / Essen, L.O. / Oesterhelt, D.
History
DepositionJun 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 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_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-rich dpsA-homolog protein
B: Iron-rich dpsA-homolog protein
C: Iron-rich dpsA-homolog protein
D: Iron-rich dpsA-homolog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,15818
Polymers80,4874
Non-polymers67014
Water14,340796
1
A: Iron-rich dpsA-homolog protein
B: Iron-rich dpsA-homolog protein
C: Iron-rich dpsA-homolog protein
D: Iron-rich dpsA-homolog protein
hetero molecules

A: Iron-rich dpsA-homolog protein
B: Iron-rich dpsA-homolog protein
C: Iron-rich dpsA-homolog protein
D: Iron-rich dpsA-homolog protein
hetero molecules

A: Iron-rich dpsA-homolog protein
B: Iron-rich dpsA-homolog protein
C: Iron-rich dpsA-homolog protein
D: Iron-rich dpsA-homolog protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,47354
Polymers241,46212
Non-polymers2,01142
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area67290 Å2
ΔGint-531 kcal/mol
Surface area61880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.110, 91.110, 150.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-1202-

SO4

21B-1202-

SO4

31B-1305-

FE

41C-1502-

NA

51C-1602-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 7 - 181 / Label seq-ID: 7 - 181

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe protein is dodecameric with a tetramer in the AU. The dodecamer can be constructed by simple crystallographic operations.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Iron-rich dpsA-homolog protein / Bacterioferritin dpsA


Mass: 20121.846 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: wildtype strain - TOM / References: UniProt: Q9HMP7

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Non-polymers , 5 types, 810 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG400, 1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→158 Å / Num. obs: 92251 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10
Reflection shellResolution: 1.6→1.641 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ProDCdata collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dps-protein from E. coli - PDB entry 1DPS

1dps


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.793 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21039 6766 7.2 %RANDOM
Rwork0.16484 ---
obs0.16808 87268 98.53 %-
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: 21.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0.17 Å20 Å2
2---0.33 Å20 Å2
3---0.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 22 796 6277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215555
X-RAY DIFFRACTIONr_bond_other_d0.0030.024818
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.947552
X-RAY DIFFRACTIONr_angle_other_deg0.934311174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8625701
X-RAY DIFFRACTIONr_chiral_restr0.1250.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026451
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021049
X-RAY DIFFRACTIONr_nbd_refined0.2550.21565
X-RAY DIFFRACTIONr_nbd_other0.260.25859
X-RAY DIFFRACTIONr_nbtor_other0.090.23378
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2650.2579
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.264
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.2265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.295
X-RAY DIFFRACTIONr_mcbond_it0.9521.53493
X-RAY DIFFRACTIONr_mcangle_it1.89525537
X-RAY DIFFRACTIONr_scbond_it3.80632062
X-RAY DIFFRACTIONr_scangle_it6.3084.52015
Refine LS restraints NCS

Ens-ID: 1 / Number: 2553 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.190.5
2Bmedium positional0.20.5
3Cmedium positional0.210.5
4Dmedium positional0.220.5
1Amedium thermal12
2Bmedium thermal1.062
3Cmedium thermal0.622
4Dmedium thermal0.662
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.292 474
Rwork0.276 6366
obs-6366
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)
10.29860.00410.03790.2032-0.01960.1943-0.00130.0631-0.0396-0.06950.0230.11320-0.0917-0.02160.03310.0117-0.00930.01210.01070.0273.95419.42710.771
20.3937-0.08860.10220.0747-0.0450.0928-0.00030.0957-0.069-0.03040.02480.07280.0063-0.037-0.02450.0156-0.0209-0.00550.03810.01590.0169-29.15437.764-3.947
30.2986-0.05450.02810.2176-0.00050.1344-0.00930.03580.0678-0.0204-0.01140.1329-0.0578-0.0810.02070.02340.00330.00220.02620.00010.0313-10.75552.52528.945
40.2135-0.02880.01510.22770.01070.1031-0.00450.02420.0309-0.0246-0.01740.1668-0.0329-0.06890.02190.02340.00330.00220.02630.00010.0313-10.75552.52528.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1812 - 181
2X-RAY DIFFRACTION2BB7 - 1817 - 181
3X-RAY DIFFRACTION3CC7 - 1817 - 181
4X-RAY DIFFRACTION4DD7 - 1817 - 181

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