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- PDB-1jig: Dlp-2 from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 1jig
TitleDlp-2 from Bacillus anthracis
ComponentsDlp-2
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 / cytoplasm
Similarity search - Function
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 1
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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
DepositionJul 2, 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-2
B: Dlp-2
C: Dlp-2
D: Dlp-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3588
Polymers66,1344
Non-polymers2234
Water5,657314
1
A: Dlp-2
B: Dlp-2
C: Dlp-2
D: Dlp-2
hetero molecules

A: Dlp-2
B: Dlp-2
C: Dlp-2
D: Dlp-2
hetero molecules

A: Dlp-2
B: Dlp-2
C: Dlp-2
D: Dlp-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,07324
Polymers198,40312
Non-polymers67012
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 area34410 Å2
ΔGint-401 kcal/mol
Surface area61190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.723, 87.723, 214.875
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-2


Mass: 16533.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: dlp-2 / Plasmid: pSM214G / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q8RPQ1
#2: Chemical
ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 314 / 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: Citrete buffer, ammonuium acetate, 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
320 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. all: 105192 / Num. obs: 105192 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 12.7
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9 / Num. unique all: 13823 / % possible all: 88.2
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 3 % / Rmerge(I) obs: 0.032
Reflection shell
*PLUS
% possible obs: 88.2 % / Num. unique obs: 13823 / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9

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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

Resolution: 1.46→71.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2406290.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Details: The crystal presents a nearly perfect twinning. The refinement was carried on with the twinning procedure of CNS, with the twinning law h,-h-k,-l.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 10102 9.6 %RANDOM
Rwork0.186 ---
obs0.186 105192 98 %-
all-105192 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.65 Å2 / ksol: 0.443 e/Å3
Displacement parametersBiso mean: 11.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.38 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.46→71.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 4 314 4974
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it0.9991.5
X-RAY DIFFRACTIONc_mcangle_it1.432
X-RAY DIFFRACTIONc_scbond_it2.3262
X-RAY DIFFRACTIONc_scangle_it3.4032.5
Refine LS restraints NCSNCS model details: CONSTR / Rms dev position: 0.016 Å / Weight Biso : 4 / Weight position: 300
LS refinement shellResolution: 1.46→1.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 1476 9.3 %
Rwork0.224 14468 -
obs-13823 89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.186 / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rfree: 0.231 / Rfactor Rwork: 0.224 / Rfactor obs: 0.224

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