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- PDB-4m32: Crystal structure of gated-pore mutant D138N of second DNA-Bindin... -

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Basic information

Entry
Database: PDB / ID: 4m32
TitleCrystal structure of gated-pore mutant D138N of second DNA-Binding protein under starvation from Mycobacterium smegmatis
ComponentsPutative starvation-induced DNA protecting protein/Ferritin and Dps
KeywordsDNA BINDING PROTEIN / ferritin-like fold / ferroxidation / Iron
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 (bacteria)
MethodX-RAY DIFFRACTION / Direct refinement against model PDB / Resolution: 1.86 Å
AuthorsWilliams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: A histidine aspartate ionic lock gates the iron passage in miniferritins from Mycobacterium smegmatis
Authors: Williams, S.M. / Chandran, A.V. / Vijayabaskar, M.S. / Roy, S. / Balaram, H. / Vishveshwara, S. / Vijayan, M. / Chatterji, D.
History
DepositionAug 6, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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

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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)74,41413
Polymers74,0474
Non-polymers3679
Water7,530418
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)223,24239
Polymers222,14012
Non-polymers1,10227
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 area52700 Å2
ΔGint26 kcal/mol
Surface area57990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.650, 89.650, 421.071
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-201-

MG

21A-202-

CL

31D-201-

MG

41A-352-

HOH

51A-359-

HOH

61D-302-

HOH

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Components

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


Mass: 18511.699 Da / Num. of mol.: 4 / Mutation: D138N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: DPS2, MSMEG_3242, MSMEI_3159 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QXB7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 6.5
Details: 150mM MgCl2, 0.1M sodium cacodylate, 20% PEG3350, pH 6.5, Microbatch under oil, temperature 298K

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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: Aug 27, 2011 / Details: mirrors
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.85→43.57 Å / Num. obs: 55022 / Redundancy: 4.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 5.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Direct refinement against model PDB
Starting model: 2z90

2z90


Resolution: 1.86→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.557 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20759 2791 5.1 %RANDOM
Rwork0.1804 ---
obs0.1818 52213 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.19 Å20 Å2
2--0.37 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.86→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 9 418 5395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0215129
X-RAY DIFFRACTIONr_angle_refined_deg0.8151.9486993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1895662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.72823.977259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82115850
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9661552
X-RAY DIFFRACTIONr_chiral_restr0.060.2820
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213968
X-RAY DIFFRACTIONr_mcbond_it0.2861.53245
X-RAY DIFFRACTIONr_mcangle_it0.57525248
X-RAY DIFFRACTIONr_scbond_it0.9831884
X-RAY DIFFRACTIONr_scangle_it1.7124.51739
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 206 -
Rwork0.291 3629 -
obs--95.68 %

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