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- PDB-3gfj: Crystal structure of the ST1710 mutant (R89A) protein -

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Basic information

Entry
Database: PDB / ID: 3gfj
TitleCrystal structure of the ST1710 mutant (R89A) protein
Components146aa long hypothetical transcriptional regulator
KeywordsTRANSCRIPTION / Transcription regulator / ST1710 / MarR / DNA-binding / Transcription regulation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
MarR family / : / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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
MarR family transcriptional regulator
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsKumarevel, T. / Tanaka, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: Nucleic Acids Res. / Year: 2009
Title: ST1710-DNA complex crystal structure reveals the DNA binding mechanism of the MarR family of regulators.
Authors: Kumarevel, T. / Tanaka, T. / Umehara, T. / Yokoyama, S.
#1: Journal: J.Struct.Biol. / Year: 2008
Title: Crystal structure of the MarR family regulatory protein, ST1710, from Sulfolobus tokodaii strain 7.
Authors: Kumarevel, T. / Tanaka, T. / Nishio, M. / Gopinath, S.C. / Takio, K. / Shinkai, A. / Kumar, P.K. / Yokoyama, S.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 146aa long hypothetical transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8342
Polymers16,7931
Non-polymers401
Water2,252125
1
A: 146aa long hypothetical transcriptional regulator
hetero molecules

A: 146aa long hypothetical transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6674
Polymers33,5872
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6150 Å2
ΔGint-43 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.862, 45.862, 138.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein 146aa long hypothetical transcriptional regulator / Transcription regulator ST1710


Mass: 16793.449 Da / Num. of mol.: 1 / Mutation: R89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Gene: ST1710 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CodonPlus (DE3)-RIL-X / References: UniProt: Q96ZY1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG 8000, 0.2M Calcium acetate, 0.1M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 8143 / Num. obs: 8143 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.091
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 13 % / Num. unique all: 783 / Rsym value: 0.389 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4AutoMolrepphasing
RefinementStarting model: 2EB7

2eb7


Resolution: 2.2→19.66 Å / Rfactor Rfree error: 0.01 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 63932 / 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
Rfree0.245 585 7.4 %RANDOM
Rwork0.201 ---
obs0.201 7877 97.6 %-
all-8143 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.432 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 75.82 Å2 / Biso mean: 28.066 Å2 / Biso min: 10.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.12 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1136 0 1 125 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.247 88 7 %
Rwork0.202 1162 -
all-1250 -
obs--96.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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