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- PDB-2z90: Crystal Structure of the Second Dps from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 2z90
TitleCrystal Structure of the Second Dps from Mycobacterium smegmatis
ComponentsStarvation-inducible DNA-binding protein or fine tangled pili major subunit
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / QUARTERNARY ASSEMBLY / FERROXIDATION
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: 2.4 Å
AuthorsRoy, S. / Saraswathi, R. / Chatterji, D. / Vijayan, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function.
Authors: Roy, S. / Saraswathi, R. / Chatterji, D. / Vijayan, M.
History
DepositionSep 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
B: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
C: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
D: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,76212
Polymers71,4194
Non-polymers3438
Water7,422412
1
A: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
B: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
C: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
D: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
hetero molecules

A: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
B: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
C: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
D: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
hetero molecules

A: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
B: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
C: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
D: Starvation-inducible DNA-binding protein or fine tangled pili major subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,28736
Polymers214,25812
Non-polymers1,02924
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 area55020 Å2
ΔGint-209.4 kcal/mol
Surface area57450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.008, 90.008, 421.522
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-163-

MG

21A-164-

CL

31A-263-

HOH

41D-256-

HOH

51D-257-

HOH

61D-258-

HOH

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Components

#1: Protein
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)
Species: Mycobacterium smegmatis / Strain: MC(2)155 / Gene: MSMEG_3242 / Plasmid: pETMsDps2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: A0QXB7
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: microbatch method under oil / pH: 6.5
Details: 20mM Tris-HCl (pH 7.9), 200 mM NaCl, PEG-3000, 200mM MgCl2, 0.1M sodium cacodylate (pH 6.5), Microbatch method under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2006 / Details: mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 26434 / % possible obs: 99.9 % / Redundancy: 17.2 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.143 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 2584 / Rsym value: 0.48 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9R

1o9r


Resolution: 2.4→29.94 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4171381.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1276 4.8 %RANDOM
Rwork0.187 ---
obs0.187 26434 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.079 Å2 / ksol: 0.323615 e/Å3
Displacement parametersBiso mean: 27.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å22.55 Å20 Å2
2--3.13 Å20 Å2
3----6.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4973 0 8 412 5393
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 207 4.8 %
Rwork0.212 4104 -
obs-4104 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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