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- PDB-2it0: Crystal structure of a two-domain IdeR-DNA complex crystal form II -

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Basic information

Entry
Database: PDB / ID: 2it0
TitleCrystal structure of a two-domain IdeR-DNA complex crystal form II
Components
  • (mbtA/mbtB operator strand ...) x 2
  • Iron-dependent repressor ideR
KeywordsTRANSCRIPTION/DNA / DNA-binding protein / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity ...catechol-containing siderophore biosynthetic process / cobalt ion binding / cadmium ion binding / nickel cation binding / transition metal ion binding / peptidoglycan-based cell wall / ferrous iron binding / manganese ion binding / response to oxidative stress / protein dimerization activity / iron ion binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / FeoA domain / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain ...Diphteria toxin repressor, SH3 domain / Diphteria toxin repressor SH3 domain / FeoA domain / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Diphtheria Toxin Repressor; domain 2 / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / DNA / DNA (> 10) / Iron-dependent repressor IdeR / Iron-dependent repressor IdeR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWisedchaisri, G. / Chou, C.J. / Wu, M. / Roach, C. / Rice, A.E. / Holmes, R.K. / Beeson, C. / Hol, W.G.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structures, metal activation, and DNA-binding properties of two-domain IdeR from Mycobacterium tuberculosis
Authors: Wisedchaisri, G. / Chou, C.J. / Wu, M. / Roach, C. / Rice, A.E. / Holmes, R.K. / Beeson, C. / Hol, W.G.
History
DepositionOct 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ncs_dom_lim / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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

Downloads & links

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Assembly

Deposited unit
E: mbtA/mbtB operator strand 1
F: mbtA/mbtB operator strand 2
A: Iron-dependent repressor ideR
B: Iron-dependent repressor ideR
C: Iron-dependent repressor ideR
D: Iron-dependent repressor ideR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,01728
Polymers91,7226
Non-polymers1,29522
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.009, 70.363, 79.569
Angle α, β, γ (deg.)108.950, 103.080, 94.840
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLYGLYAC3 - 1393 - 139
21GLUGLUGLYGLYBD3 - 1393 - 139
31GLUGLUGLYGLYCE3 - 1393 - 139
41GLUGLUGLYGLYDF3 - 1393 - 139
12VALVALPHEPHEAC140 - 147140 - 147
22VALVALPHEPHEBD140 - 147140 - 147

NCS ensembles :
ID
1
2
DetailsThe asymmetric unit contains one biological double-dimer two-domain IdeR-DNA complex

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Components

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MbtA/mbtB operator strand ... , 2 types, 2 molecules EF

#1: DNA chain mbtA/mbtB operator strand 1


Mass: 10112.492 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain mbtA/mbtB operator strand 2


Mass: 10188.573 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 4 molecules ABCD

#3: Protein
Iron-dependent repressor ideR


Mass: 17855.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: IdeR,dtxR / Plasmid: pAER36 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0A672, UniProt: P9WMH1*PLUS

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Non-polymers , 3 types, 55 molecules

#4: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ni
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.97 Å3/Da / Density % sol: 58.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26% PEG 4000, 0.2 M sodium acetate, 0.1 M Tris HCl pH 8.5, 5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Na acetate11
3Tris HCl11
4PEG 400012
5Na acetate12
6Tris HCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1217 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1217 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Av σ(I) over netI: 3.8 / Number: 59087 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / D res high: 2.6 Å / D res low: 72.481 Å / Num. obs: 31514 / % possible obs: 96.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.2237.9197.210.0530.0531.9
5.818.2298.110.0550.0552
4.755.819610.1510.1511.6
4.114.7596.210.0820.0821.8
3.684.1196.110.0630.0631.9
3.363.6896.510.0870.0871.9
3.113.3696.510.1080.1081.9
2.913.1196.310.2070.2071.9
2.742.919610.2630.2631.9
2.62.7495.910.3480.3481.9
ReflectionResolution: 2.6→72.481 Å / Num. obs: 31514 / % possible obs: 96.3 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.741.90.3482874645850.34895.9
2.74-2.911.90.2632.8827243450.26396
2.91-3.111.90.2073.5778840930.20796.3
3.11-3.361.90.1086.8722938210.10896.5
3.36-3.681.90.0877.9654334930.08796.5
3.68-4.111.90.06311.1599031880.06396.1
4.11-4.751.80.0827.9506227860.08296.2
4.75-5.811.60.1512.2386223460.15196
5.81-8.2220.05513.2363518500.05598.1
8.22-37.911.90.05310.3196010070.05397.2

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Phasing

Phasing MRRfactor: 0.354 / Cor.coef. Fo:Fc: 0.701
Highest resolutionLowest resolution
Rotation3 Å37.91 Å
Translation3 Å37.91 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ISZ

2isz


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.852 / SU B: 10.597 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1595 5.1 %RANDOM
Rwork0.226 ---
obs0.229 31507 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.09 Å21.63 Å2
2---0.16 Å2-0.32 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 1347 52 33 5916
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0216128
X-RAY DIFFRACTIONr_angle_refined_deg1.192.2638534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7235560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.17322.694219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.98615820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7561560
X-RAY DIFFRACTIONr_chiral_restr0.0680.2978
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024143
X-RAY DIFFRACTIONr_nbd_refined0.2460.32798
X-RAY DIFFRACTIONr_nbtor_refined0.3240.54060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5394
X-RAY DIFFRACTIONr_metal_ion_refined0.0380.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.58
X-RAY DIFFRACTIONr_mcbond_it0.93532901
X-RAY DIFFRACTIONr_mcangle_it1.5444571
X-RAY DIFFRACTIONr_scbond_it0.94634008
X-RAY DIFFRACTIONr_scangle_it1.42443963
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1089LOOSE POSITIONAL0.545
12B1089LOOSE POSITIONAL0.575
13C1089LOOSE POSITIONAL0.55
14D1089LOOSE POSITIONAL0.445
11A1089LOOSE THERMAL3.1310
12B1089LOOSE THERMAL3.9210
13C1089LOOSE THERMAL3.4310
14D1089LOOSE THERMAL2.8410
21A62LOOSE POSITIONAL0.585
21A62LOOSE THERMAL1.2210
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 131 -
Rwork0.302 2184 -
obs-2315 95.78 %

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