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- PDB-4o6j: Crystal sturucture of T. acidophilum IdeR -

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Basic information

Entry
Database: PDB / ID: 4o6j
TitleCrystal sturucture of T. acidophilum IdeR
ComponentsIron-dependent transcription repressor related protein
KeywordsMETAL BINDING PROTEIN / Irod dependent transcription factor / Fe
Function / homology
Function and homology information


transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / 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 ...FeoA domain / Ferrous iron transport protein A (FeoA) / Iron dependent repressor, metal binding and dimerisation domain / Ferrous iron transporter, core domain / Ferrous iron transporter FeoA domain / FeoA / 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 / SH3 type barrels. / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Roll / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / Iron-dependent transcription repressor related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLee, J.Y. / Yeo, H.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural analysis and insight into metal-ion activation of the iron-dependent regulator from Thermoplasma acidophilum.
Authors: Yeo, H.K. / Park, Y.W. / Lee, J.Y.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-dependent transcription repressor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2953
Polymers27,1831
Non-polymers1122
Water63135
1
A: Iron-dependent transcription repressor related protein
hetero molecules

A: Iron-dependent transcription repressor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5896
Polymers54,3662
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2200 Å2
ΔGint-73 kcal/mol
Surface area19890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.215, 84.604, 46.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Iron-dependent transcription repressor related protein / IdeR


Mass: 27183.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic)
Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165
Gene: Ta0872 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HJU1
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 4000, 0.2M ammonium acetate, 0.1M sodium acetate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.7394 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7394 Å / Relative weight: 1
ReflectionResolution: 2.3→19.991 Å / Num. obs: 11321 / % possible obs: 99.1 %

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.991 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 22.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 541 4.82 %
Rwork0.1605 --
obs0.1631 11224 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1683 0 2 35 1720
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011708
X-RAY DIFFRACTIONf_angle_d1.262310
X-RAY DIFFRACTIONf_dihedral_angle_d15.14663
X-RAY DIFFRACTIONf_chiral_restr0.052272
X-RAY DIFFRACTIONf_plane_restr0.006300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.53110.23791190.1781258598
2.5311-2.89640.27191340.1832262999
2.8964-3.64550.22531440.17962668100
3.6455-19.99210.18491440.14272801100
Refinement TLS params.Method: refined / Origin x: 35.5336 Å / Origin y: 23.2902 Å / Origin z: 16.1761 Å
111213212223313233
T0.2672 Å2-0.017 Å20.0002 Å2-0.2504 Å20.0113 Å2--0.291 Å2
L0.9792 °2-0.4827 °20.4492 °2-0.58 °20.1855 °2--1.3829 °2
S0.0065 Å °-0.0281 Å °-0.0164 Å °-0.0213 Å °-0.0118 Å °0.0415 Å °0.0965 Å °0.1221 Å °-0.0004 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 7:219)

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