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

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Basic information

Entry
Database: PDB / ID: 7pzb
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*CP*G)-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
CYCLIC GUANOSINE 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: 3.12 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

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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*CP*G)-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*CP*G)-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)75,2708
Polymers74,5796
Non-polymers6902
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-68 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.710, 72.900, 199.990
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 6 and (name N or name...
d_2ens_1(chain "B" and (resid 6 through 7 or resid 9...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGSERSERAA6 - 76 - 7
d_12ALAALATRPTRPAA9 - 119 - 11
d_13SERSERLEULEUAA13 - 2513 - 25
d_14GLUGLUGLUGLUAA2727
d_15SERSERTYRTYRAA29 - 3429 - 34
d_16LYSLYSLEULEUAA36 - 6536 - 65
d_17THRTHRLEULEUAA67 - 7567 - 75
d_18HISHISTHRTHRAA78 - 12078 - 120
d_19ARGARGPROPROAA122 - 123122 - 123
d_110THRTHRALAALAAA125 - 126125 - 126
d_111ALAALAILEILEAA128 - 130128 - 130
d_112PHEPHELEULEUAA132 - 164132 - 164
d_113ILEILEGLYGLYAA167 - 169167 - 169
d_114GLUGLUASNASNAA171 - 177171 - 177
d_115ARGARGASPASPAA179 - 230179 - 230
d_116PCGPCGPCGPCGAG301
d_21ARGARGSERSERBB6 - 76 - 7
d_22ALAALATRPTRPBB9 - 119 - 11
d_23SERSERLEULEUBB13 - 2513 - 25
d_24GLUGLUGLUGLUBB2727
d_25SERSERTYRTYRBB29 - 3429 - 34
d_26LYSLYSLEULEUBB36 - 6536 - 65
d_27THRTHRLEULEUBB67 - 7567 - 75
d_28HISHISTHRTHRBB78 - 12078 - 120
d_29ARGARGPROPROBB122 - 123122 - 123
d_210THRTHRALAALABB125 - 126125 - 126
d_211ALAALAILEILEBB128 - 130128 - 130
d_212PHEPHELEULEUBB132 - 164132 - 164
d_213ILEILEGLYGLYBB167 - 169167 - 169
d_214GLUGLUASNASNBB171 - 177171 - 177
d_215ARGARGASPASPBB179 - 230179 - 230
d_216PCGPCGPCGPCGBH301

NCS oper: (Code: givenMatrix: (-0.974222926119, -0.214186500376, 0.0708084266268), (-0.221241067735, 0.845847090442, -0.485381385652), (0.0440690386994, -0.488535405726, -0.871430477537)Vector: 23. ...NCS oper: (Code: given
Matrix: (-0.974222926119, -0.214186500376, 0.0708084266268), (-0.221241067735, 0.845847090442, -0.485381385652), (0.0440690386994, -0.488535405726, -0.871430477537)
Vector: 23.0953227737, 16.0546623196, 50.6071245034)

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Components

#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) / References: UniProt: Q92SD2
#2: DNA chain DNA (5'-D(*CP*TP*AP*GP*GP*TP*AP*AP*CP*AP*TP*TP*AP*CP*TP*CP*GP*CP*G)-3')


Mass: 5804.772 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)
#4: Chemical ChemComp-PCG / CYCLIC GUANOSINE MONOPHOSPHATE


Mass: 345.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O7P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-butanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG ...Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-butanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 0.1 M MOPS/HEPES-Na pH 7.5, 12.5% (v/v) MPD, 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG3350, 0.44 mM Clr, 25 mM cGMP, 25 mM magnesium chloride, 0.55 mM dsDNA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 13, 2019
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.12→49.15 Å / Num. obs: 9719 / % possible obs: 70.19 % / Redundancy: 4.3 % / Biso Wilson estimate: 100.5 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.064 / Net I/σ(I): 11.08
Reflection shellResolution: 3.12→3.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 74 / CC1/2: 0.61 / Rrim(I) all: 0.621 / % possible all: 5.53

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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: 3.12→49.2 Å / SU ML: 0.5558 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 44.1595
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3331 469 4.83 %
Rwork0.2894 9247 -
obs0.2914 9716 69.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.23 Å2
Refinement stepCycle: LAST / Resolution: 3.12→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3466 1161 46 3 4676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00544871
X-RAY DIFFRACTIONf_angle_d1.08216834
X-RAY DIFFRACTIONf_chiral_restr0.0583788
X-RAY DIFFRACTIONf_plane_restr0.0136673
X-RAY DIFFRACTIONf_dihedral_angle_d24.75571052
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.39894657279E-11 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.570.4327710.37691154X-RAY DIFFRACTION27.01
3.57-4.50.3841840.3463616X-RAY DIFFRACTION83.19
4.5-49.20.30372140.25974477X-RAY DIFFRACTION97.93

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