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- PDB-1moj: Crystal structure of an archaeal dps-homologue from Halobacterium... -

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Basic information

Entry
Database: PDB / ID: 1moj
TitleCrystal structure of an archaeal dps-homologue from Halobacterium salinarum
ComponentsDps-like ferritin
KeywordsDNA BINDING PROTEIN / dps / ferritin / four-helix bundle / halophilic
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: 1.9 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
DepositionSep 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: 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_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_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: Dps-like ferritin
B: Dps-like ferritin
C: Dps-like ferritin
D: Dps-like ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,96616
Polymers80,4874
Non-polymers47812
Water5,350297
1
A: Dps-like ferritin
B: Dps-like ferritin
C: Dps-like ferritin
D: Dps-like ferritin
hetero molecules

A: Dps-like ferritin
B: Dps-like ferritin
C: Dps-like ferritin
D: Dps-like ferritin
hetero molecules

A: Dps-like ferritin
B: Dps-like ferritin
C: Dps-like ferritin
D: Dps-like ferritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,89748
Polymers241,46212
Non-polymers1,43536
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 area66570 Å2
ΔGint-476 kcal/mol
Surface area60980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.747, 90.747, 149.410
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-305-

FE

21C-312-

NA

31B-366-

HOH

DetailsThe biological assembly of a 23-symmetric dodecamer is generated from the tetramer in the asymmetric unit by the operations: -Y,X-Y,Z and Y-X,-X,Z

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Components

#1: Protein
Dps-like ferritin / starvation induced DNA binding protein / DpsA


Mass: 20121.846 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: TOM / References: UniProt: Q9HMP7
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 400, Tris/HCl, magnesium chloride, sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 66071 / Num. obs: 63709 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.99 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.1 / % possible all: 99.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DPS

1dps


Resolution: 1.9→29.88 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal was merohedrally twinned along the z-axis with a twinning ratio of 0.57/0.43 for relating reflections h,k,l with -h,-k,l. Refinement of the twinned crystal proceeded in CNS, but ...Details: The crystal was merohedrally twinned along the z-axis with a twinning ratio of 0.57/0.43 for relating reflections h,k,l with -h,-k,l. Refinement of the twinned crystal proceeded in CNS, but the twinned R-factors are systematically underestimated compared to the non-twinned case
RfactorNum. reflection% reflectionSelection details
Rfree0.182 5597 9.9 %SHELLS
Rwork0.147 ---
all0.151 56607 --
obs0.147 56417 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7172 Å2 / ksol: 0.427365 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0.9 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5459 0 12 297 5768
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.5
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.372.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.227 422 4.3 %
Rwork0.215 6506 -
obs-6928 99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPOLOGY_INFILE_1
X-RAY DIFFRACTION2ION.PARAMTOPOLOGY_INFILE_2
X-RAY DIFFRACTION3WATER_REP.PARAMTOPOLOGY_INFILE_3
X-RAY DIFFRACTION4TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5TOPOLOGY_INFILE_5

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