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- PDB-4r4e: Structure of GlnR-DNA complex -

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Basic information

Entry
Database: PDB / ID: 4r4e
TitleStructure of GlnR-DNA complex
Components
  • DNA (5'-D(*AP*TP*TP*CP*TP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*AP*GP*TP*A)-3')
  • HTH-type transcriptional regulator GlnR
KeywordsTranscription regulator/DNA / TnrA/GlnR family / B. subtilis / nitrogen homeostasis / new member / TnrA/GlnR DNA-binding family of winged-HTH with c-terminal inducer/sensor domain / transcription / DNA / GS-Q / Nucleoid / Transcription regulator-DNA complex
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding
Similarity search - Function
MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / 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 ...MerR family regulatory protein / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / MerR-type HTH domain signature. / 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
DNA / HTH-type transcriptional regulator GlnR
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
synthetic DNA (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.57 Å
AuthorsSchumacher, M.A.
CitationJournal: Genes Dev. / Year: 2015
Title: Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Authors: Schumacher, M.A. / Chinnam, N.B. / Cuthbert, B. / Tonthat, N.K. / Whitfill, T.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HTH-type transcriptional regulator GlnR
A: HTH-type transcriptional regulator GlnR
D: DNA (5'-D(*AP*TP*TP*CP*TP*GP*AP*CP*A)-3')
E: DNA (5'-D(*TP*GP*TP*CP*AP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7445
Polymers24,5234
Non-polymers2211
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.350, 103.300, 137.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein HTH-type transcriptional regulator GlnR


Mass: 9683.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: glnR, BSU17450 / Production host: Escherichia coli (E. coli) / References: UniProt: P37582
#2: DNA chain DNA (5'-D(*AP*TP*TP*CP*TP*GP*AP*CP*A)-3')


Mass: 2714.811 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cognate DNA / Source: (synth.) synthetic DNA (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*CP*AP*GP*TP*A)-3')


Mass: 2441.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: cognate DNA (complement to 2) / Source: (synth.) synthetic DNA (others)
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 5.51 Å3/Da / Density % sol: 77.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 40% PEG 400, 0.1 M CAPS, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9790, 0.97999, 0.9250
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2013 / Details: Si(111)
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979991
30.9251
ReflectionResolution: 2.52→82.5 Å / Num. all: 17500 / Num. obs: 17350 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rsym value: 0.041 / Net I/σ(I): 18.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.15data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: Same crystal form but selenomet substituted. This starting model was used for final refinement with the 2.52 A native data

Resolution: 2.57→82.5 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 2571 14.6 %random
Rwork0.2543 ---
all0.256 17350 --
obs0.2543 17019 96.4 %-
Solvent computationBsol: 93.0714 Å2
Displacement parametersBiso max: 187.7 Å2 / Biso mean: 82.7887 Å2 / Biso min: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1-26.001 Å20 Å20 Å2
2---30.554 Å20 Å2
3---4.553 Å2
Refinement stepCycle: LAST / Resolution: 2.57→82.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1350 342 14 50 1756
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.069
X-RAY DIFFRACTIONc_mcbond_it4.2991.5
X-RAY DIFFRACTIONc_scbond_it6.2192
X-RAY DIFFRACTIONc_mcangle_it6.5962
X-RAY DIFFRACTIONc_scangle_it8.9182.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5caps.param.txtcaps.top

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