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- PDB-7pza: Structure of the Clr-cAMP-DNA complex -

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Basic information

Entry
Database: PDB / ID: 7pza
TitleStructure of the Clr-cAMP-DNA complex
Components
  • DNA (5'-D(*CP*TP*AP*GP*GP*TP*AP*AP*CP*AP*TP*TP*AP*CP*TP*CP*GP)-3')
  • DNA (5'-D(*GP*CP*GP*AP*GP*TP*AP*AP*TP*GP*TP*TP*AP*C)-3')
  • Putative cAMP-binding protein-catabolite gene activator
KeywordsSIGNALING PROTEIN / cyclic nucleotide / second messenger / transcription factor / CRP family
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily ...Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / DNA / DNA (> 10) / Putative cAMP-binding protein-catabolite gene activator
Similarity search - Component
Biological speciesSinorhizobium meliloti 1021 (bacteria)
Sinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsWerel, L. / Essen, L.-O.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP1879 Germany
CitationJournal: Mbio / Year: 2023
Title: Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein.
Authors: Werel, L. / Farmani, N. / Krol, E. / Serrania, J. / Essen, L.O. / Becker, A.
History
DepositionOct 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cAMP-binding protein-catabolite gene activator
B: Putative cAMP-binding protein-catabolite gene activator
C: DNA (5'-D(*CP*TP*AP*GP*GP*TP*AP*AP*CP*AP*TP*TP*AP*CP*TP*CP*GP)-3')
D: DNA (5'-D(*GP*CP*GP*AP*GP*TP*AP*AP*TP*GP*TP*TP*AP*C)-3')
E: DNA (5'-D(*CP*TP*AP*GP*GP*TP*AP*AP*CP*AP*TP*TP*AP*CP*TP*CP*GP)-3')
F: DNA (5'-D(*GP*CP*GP*AP*GP*TP*AP*AP*TP*GP*TP*TP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,62810
Polymers73,9216
Non-polymers7074
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.100, 69.930, 200.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 9 through 27 or resid 30...
d_2ens_1(chain "B" and (resid 9 through 26 or (resid 27...
d_1ens_2chain "a"
d_2ens_2chain "b"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAGLUGLUAA9 - 279 - 27
d_12ens_1GLYGLYTYRTYRAA30 - 3430 - 34
d_13ens_1LYSLYSLEULEUAA36 - 6536 - 65
d_14ens_1THRTHRLEULEUAA67 - 16467 - 164
d_15ens_1ILEILESERSERAA167 - 170167 - 170
d_16ens_1METMETASNASNAA172 - 199172 - 199
d_17ens_1ALAALAILEILEAA201 - 211201 - 211
d_18ens_1ARGARGGLYGLYAA213 - 223213 - 223
d_19ens_1LEULEUPROPROAA225 - 231225 - 231
d_21ens_1ALAALAGLUGLUBB9 - 279 - 27
d_22ens_1GLYGLYTYRTYRBB30 - 3430 - 34
d_23ens_1LYSLYSLEULEUBB36 - 6536 - 65
d_24ens_1THRTHRLEULEUBB67 - 16467 - 164
d_25ens_1ILEILESERSERBB167 - 170167 - 170
d_26ens_1METMETASNASNBB172 - 199172 - 199
d_27ens_1ALAALAILEILEBB201 - 211201 - 211
d_28ens_1ARGARGGLYGLYBB213 - 223213 - 223
d_29ens_1LEULEUPROPROBB225 - 231225 - 231
d_11ens_2CMPCMPCMPCMPAG301
d_21ens_2CMPCMPCMPCMPBI301

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.968594893109, -0.231728822067, 0.090142587413), (-0.246173236389, 0.842746877541, -0.478723759678), (0.0349667088501, -0.485880081314, -0.873325755863)22.8969953837, 16.29838839, 50.8609445625
2given(-0.95294621959, -0.290094267133, 0.087970556133), (-0.288767730046, 0.780408751167, -0.554594788279), (0.09223177681, -0.5539020647, -0.827457432179)23.5475287188, 19.282785913, 50.5150346974

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative cAMP-binding protein-catabolite gene activator


Mass: 27165.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 1021 (bacteria) / Gene: SMc02175 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q92SD2

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*CP*TP*AP*GP*GP*TP*AP*AP*CP*AP*TP*TP*AP*CP*TP*CP*GP)-3')


Mass: 5475.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Sinorhizobium meliloti (bacteria)
#3: DNA chain DNA (5'-D(*GP*CP*GP*AP*GP*TP*AP*AP*TP*GP*TP*TP*AP*C)-3')


Mass: 4319.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Sinorhizobium meliloti (bacteria)

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Non-polymers , 3 types, 9 molecules

#4: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.09 M sodium fluoride, 0.09 M sodium bromide, 0.09 M sodium iodide, 0.1 M Tris base/BICINE pH 8.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG3350, 0.25 mM Clr, 25 mM cAMP, 25 mM ...Details: 0.09 M sodium fluoride, 0.09 M sodium bromide, 0.09 M sodium iodide, 0.1 M Tris base/BICINE pH 8.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG3350, 0.25 mM Clr, 25 mM cAMP, 25 mM magnesium chloride, 0.3125 mM dsDNA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2018
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.722→66.03 Å / Num. obs: 14734 / % possible obs: 74.89 % / Redundancy: 9.3 % / Biso Wilson estimate: 64.8 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.1453 / Rpim(I) all: 0.0496 / Rrim(I) all: 0.154 / Net I/σ(I): 11.35
Reflection shellResolution: 2.722→2.819 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.223 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 129 / CC1/2: 0.788 / CC star: 0.939 / Rpim(I) all: 0.4727 / Rrim(I) all: 1.315 / % possible all: 6.72

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CYD

4cyd


Resolution: 2.72→66.03 Å / SU ML: 0.4294 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.3425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3039 747 5.07 %
Rwork0.2706 13983 -
obs0.2723 14730 74.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.05 Å2
Refinement stepCycle: LAST / Resolution: 2.72→66.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 1079 46 5 4588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02064770
X-RAY DIFFRACTIONf_angle_d2.34756681
X-RAY DIFFRACTIONf_chiral_restr0.1135768
X-RAY DIFFRACTIONf_plane_restr0.0434668
X-RAY DIFFRACTIONf_dihedral_angle_d27.81231031
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONNCS constraints0.0736438996568
ens_2d_2BX-RAY DIFFRACTIONNCS constraints0
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.930.7208220.4329486X-RAY DIFFRACTION13.21
2.93-3.230.36871280.35742153X-RAY DIFFRACTION59.14
3.23-3.690.36932060.31893683X-RAY DIFFRACTION99.85
3.69-4.650.2932080.25573727X-RAY DIFFRACTION99.92
4.65-66.030.26111830.2413934X-RAY DIFFRACTION99.88

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