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- PDB-4o5v: Crystal structure of T. acidophilum IdeR -

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Basic information

Entry
Database: PDB / ID: 4o5v
TitleCrystal structure of T. acidophilum IdeR
ComponentsIron-dependent transcription repressor related protein
KeywordsMETAL BINDING PROTEIN / IdeR
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 / : / Diphtheria Toxin Repressor; domain 2 / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor ...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 / : / Diphtheria Toxin Repressor; domain 2 / 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 / Transcriptional repressor, C-terminal / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Winged helix DNA-binding domain superfamily / 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: 2.1 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 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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.pdbx_leaving_atom_flag / _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_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: Iron-dependent transcription repressor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6233
Polymers27,5111
Non-polymers1122
Water2,000111
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)55,2466
Polymers55,0232
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2130 Å2
ΔGint-72 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.198, 84.978, 47.078
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: 27511.268 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.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 4000, 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: 5C (4A) / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 14925 / % possible obs: 99.9 % / Observed criterion σ(I): 2

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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: 2.1→34.166 Å / SU ML: 0.22 / σ(F): 1.36 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 754 5.06 %
Rwork0.182 --
obs0.182 14888 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→34.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 2 111 1802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091709
X-RAY DIFFRACTIONf_angle_d1.192309
X-RAY DIFFRACTIONf_dihedral_angle_d14.312662
X-RAY DIFFRACTIONf_chiral_restr0.048272
X-RAY DIFFRACTIONf_plane_restr0.006300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1005-2.26260.2581720.17972758
2.2626-2.49030.28341610.18762767
2.4903-2.85050.28011400.18422784
2.8505-3.59070.23651370.1722860
3.5907-34.17020.15911440.14852965
Refinement TLS params.Method: refined / Origin x: 35.5995 Å / Origin y: 23.5046 Å / Origin z: 16.2474 Å
111213212223313233
T0.1441 Å2-0.0181 Å2-0.0013 Å2-0.119 Å20.013 Å2--0.1646 Å2
L1.382 °2-0.4783 °20.3069 °2-0.6614 °20.0961 °2--1.5851 °2
S-0.0202 Å °-0.0352 Å °-0.0496 Å °-0.0364 Å °-0.0025 Å °0.0268 Å °0.0325 Å °0.1206 Å °0.0002 Å °
Refinement TLS groupSelection details: (CHAIN A AND RESSEQ 6:218)

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