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- PDB-5z49: Crystal structure of the effector-binding domain of Synechococcus... -

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Basic information

Entry
Database: PDB / ID: 5z49
TitleCrystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose-1,5-bisphosphate
ComponentsHTH-type transcriptional activator CmpR
KeywordsTRANSCRIPTION / transcription factor / cyanobacteria
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RIBULOSE-1,5-DIPHOSPHATE / HTH-type transcriptional activator CmpR
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.148 Å
AuthorsJiang, Y.L. / Mahounga, D.M. / Sun, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001 China
National Natural Science Foundation of China31500598 China
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the effector-binding domain of Synechococcus elongatus CmpR in complex with ribulose 1,5-bisphosphate.
Authors: Mahounga, D.M. / Sun, H. / Jiang, Y.L.
History
DepositionJan 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: HTH-type transcriptional activator CmpR
A: HTH-type transcriptional activator CmpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8803
Polymers52,5702
Non-polymers3101
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-21 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.570, 86.700, 87.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HTH-type transcriptional activator CmpR


Mass: 26284.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Strain: PCC 7942 / Gene: cmpR, Synpcc7942_1310 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9F1R2
#2: Sugar ChemComp-RUB / RIBULOSE-1,5-DIPHOSPHATE


Type: saccharide / Mass: 310.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H12O11P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.25 Å3/Da / Density % sol: 45.38 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 25% tert-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 26386 / % possible obs: 99.3 % / Redundancy: 4.8 % / Net I/σ(I): 14.68
Reflection shellResolution: 1.89→1.96 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2V

5y2v


Resolution: 2.148→43.35 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.31 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2406 1326 5.03 %RANDOM
Rwork0.1881 ---
obs0.1908 26386 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.148→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 18 189 3643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083535
X-RAY DIFFRACTIONf_angle_d1.1484815
X-RAY DIFFRACTIONf_dihedral_angle_d10.8432107
X-RAY DIFFRACTIONf_chiral_restr0.065548
X-RAY DIFFRACTIONf_plane_restr0.008629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1485-2.23450.26241190.21642742X-RAY DIFFRACTION99
2.2345-2.33620.24561440.20342749X-RAY DIFFRACTION100
2.3362-2.45940.26511450.20762754X-RAY DIFFRACTION100
2.4594-2.61340.26511570.20652766X-RAY DIFFRACTION100
2.6134-2.81520.25581320.21482776X-RAY DIFFRACTION100
2.8152-3.09840.3091650.21322755X-RAY DIFFRACTION100
3.0984-3.54660.25741290.22812X-RAY DIFFRACTION100
3.5466-4.46760.21641650.16472817X-RAY DIFFRACTION100
4.4676-43.35880.20661700.16372889X-RAY DIFFRACTION98

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