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- PDB-5ww3: Crystal structure of the second DNA-Binding protein under starvat... -

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Basic information

Entry
Database: PDB / ID: 5ww3
TitleCrystal structure of the second DNA-Binding protein under starvation from Mycobacterium smegmatis soaked with iron in the ratio of 24 iron atoms per dodecamer
ComponentsPutative starvation-induced DNA protecting protein/Ferritin and Dps
KeywordsDNA BINDING PROTEIN / ferritin-like fold / DNA binding / ferroxidation / OXIDOREDUCTASE
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / DNA binding
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
: / : / Starvation-inducible DNA-binding protein or fine tangled pili major subunit
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsWilliams, S.M. / Chatterji, D.
CitationJournal: Metallomics / Year: 2017
Title: Flexible aspartates propel iron to the ferroxidation sites along pathways stabilized by a conserved arginine in Dps proteins from Mycobacterium smegmatis
Authors: Williams, S.M. / Chatterji, D.
History
DepositionDec 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / pdbx_struct_special_symmetry / struct_conn
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_alt_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.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_alt_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.pdbx_ptnr1_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative starvation-induced DNA protecting protein/Ferritin and Dps
B: Putative starvation-induced DNA protecting protein/Ferritin and Dps
C: Putative starvation-induced DNA protecting protein/Ferritin and Dps
D: Putative starvation-induced DNA protecting protein/Ferritin and Dps
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09718
Polymers71,4194
Non-polymers67814
Water7,710428
1
A: Putative starvation-induced DNA protecting protein/Ferritin and Dps
B: Putative starvation-induced DNA protecting protein/Ferritin and Dps
C: Putative starvation-induced DNA protecting protein/Ferritin and Dps
D: Putative starvation-induced DNA protecting protein/Ferritin and Dps
hetero molecules

A: Putative starvation-induced DNA protecting protein/Ferritin and Dps
B: Putative starvation-induced DNA protecting protein/Ferritin and Dps
C: Putative starvation-induced DNA protecting protein/Ferritin and Dps
D: Putative starvation-induced DNA protecting protein/Ferritin and Dps
hetero molecules

A: Putative starvation-induced DNA protecting protein/Ferritin and Dps
B: Putative starvation-induced DNA protecting protein/Ferritin and Dps
C: Putative starvation-induced DNA protecting protein/Ferritin and Dps
D: Putative starvation-induced DNA protecting protein/Ferritin and Dps
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,29254
Polymers214,25812
Non-polymers2,03442
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 area57540 Å2
ΔGint-383 kcal/mol
Surface area56210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.170, 90.170, 420.411
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-204-

MG

21A-205-

CL

31D-203-

FE2

41D-204-

FE2

51A-301-

HOH

61A-407-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative starvation-induced DNA protecting protein/Ferritin and Dps / MsDps2 / Starvation-inducible DNA-binding protein or fine tangled pili major subunit


Mass: 17854.863 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEG_3242, MSMEI_3159 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QXB7

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Non-polymers , 5 types, 442 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-FE2 / FE (II) ION


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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 6
Details: 100 mM sodium cacodylate, 150 mM MgCl2, 20% PEG3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.03→47.61 Å / Num. obs: 41744 / % possible obs: 96.8 % / Redundancy: 8.2 % / Net I/σ(I): 27.1
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 12.4 / % possible all: 78.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2z90

2z90


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.333 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19939 2116 5.1 %RANDOM
Rwork0.16424 ---
obs0.16602 39614 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 14 428 5420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.957024
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9355672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68924.091264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31915850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2091552
X-RAY DIFFRACTIONr_chiral_restr0.0870.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213992
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.3692604
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.172.0453259
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7171.4382537
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.50611.5398540
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: 2.047→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 141 -
Rwork0.185 2483 -
obs--86.03 %

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