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- PDB-3gpv: Crystal structure of a transcriptional regulator, MerR family fro... -

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Basic information

Entry
Database: PDB / ID: 3gpv
TitleCrystal structure of a transcriptional regulator, MerR family from Bacillus thuringiensis
ComponentsTranscriptional regulator, MerR family
Keywordstranscription regulator / transcriptional regulator / MerR family / Protein Structure Initiative II(PSI II) / NYSGXRC / 11183m / Structural Genomics / New York SGX Research Center for Structural Genomics / DNA-binding
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Putative DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, MerR family
Similarity search - Component
Biological speciesBacillus thuringiensis serovar konkukian (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPalani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a transcriptional regulator, MerR family from Bacillus thuringiensis
Authors: Palani, K. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, MerR family
B: Transcriptional regulator, MerR family


Theoretical massNumber of molelcules
Total (without water)35,7952
Polymers35,7952
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-30 kcal/mol
Surface area14180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.091, 39.175, 52.283
Angle α, β, γ (deg.)85.64, 85.13, 78.73
Int Tables number1
Space group name H-MP1
DetailsDIMER

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Components

#1: Protein Transcriptional regulator, MerR family


Mass: 17897.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus thuringiensis serovar konkukian (bacteria)
Gene: BT9727_1615 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6HKH9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium chloride hexahydrate 0.1M Tris hydrochloride 30% Polyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2009 / Details: MIRRORS
RadiationMonochromator: GRAPHITE Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→37.26 Å / Num. all: 21114 / Num. obs: 21114 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 2 / Num. unique all: 942 / % possible all: 49.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 204997.19 / 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
Rfree0.288 987 4.9 %RANDOM
Rwork0.268 ---
all0.266 21114 --
obs0.268 20315 87.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.6475 Å2 / ksol: 0.381566 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-3.64 Å21.81 Å2
2---2.03 Å21.6 Å2
3---3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.9→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 0 147 2083
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 109 5.3 %
Rwork0.361 1962 -
obs-942 53.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5gol.top

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