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- PDB-1ji5: Dlp-1 from bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 1ji5
TitleDlp-1 from bacillus anthracis
ComponentsDlp-1
KeywordsMETAL TRANSPORT / dodecamer / four-helix bundle
Function / homology
Function and homology information


Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / DNA binding / cytoplasm
Similarity search - Function
Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily ...Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / 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 2
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPapinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Structure of two iron-binding proteins from Bacillus anthracis.
Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M.
#2: Journal: Nat.Struct.Biol. / Year: 2000
Title: The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron-binding Site
Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D.
History
DepositionJun 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dlp-1
B: Dlp-1
C: Dlp-1
D: Dlp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0459
Polymers65,7034
Non-polymers3425
Water2,684149
1
A: Dlp-1
B: Dlp-1
C: Dlp-1
D: Dlp-1
hetero molecules

A: Dlp-1
B: Dlp-1
C: Dlp-1
D: Dlp-1
hetero molecules

A: Dlp-1
B: Dlp-1
C: Dlp-1
D: Dlp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,13427
Polymers197,10912
Non-polymers1,02515
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area37190 Å2
ΔGint-437 kcal/mol
Surface area57910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.224, 89.224, 210.165
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z

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Components

#1: Protein
Dlp-1


Mass: 16425.777 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: dlp-1 / Plasmid: pSM214G / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q8RPQ2
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium acetate, citrate buffer, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium acetate1reservoir
20.1 Mcitrate1reservoirpH5.6
330 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 12, 2001
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 20677 / Num. obs: 20677 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3107 / % possible all: 98
Reflection
*PLUS
Lowest resolution: 50 Å / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 3107 / Rmerge(I) obs: 0.38

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HP-NAP model

Resolution: 2.5→21.26 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2598111.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Non-crystallographic symmetrry was imposed to the four subunits during the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1414 6.8 %RANDOM
Rwork0.226 ---
obs0.226 20676 95.7 %-
all-20676 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.39 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å25.52 Å20 Å2
2--3.47 Å20 Å2
3----6.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 12 149 4773
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.9172
X-RAY DIFFRACTIONc_mcangle_it2.9913
X-RAY DIFFRACTIONc_scbond_it3.3133
X-RAY DIFFRACTIONc_scangle_it4.6294
Refine LS restraints NCSNCS model details: CONSTR / Rms dev position: 0.032 Å / Weight Biso : 10 / Weight position: 300
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 236 6.7 %
Rwork0.32 3280 -
obs-3107 97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4MPD.PARAM
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å / Rfactor obs: 0.226 / Rfactor Rfree: 0.291 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it3
X-RAY DIFFRACTIONc_mcangle_it3
X-RAY DIFFRACTIONc_scangle_it4
LS refinement shell
*PLUS
Rfactor Rfree: 0.326 / Rfactor Rwork: 0.32 / Rfactor obs: 0.32

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