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- PDB-3n53: Crystal structure of a response regulator receiver modulated digu... -

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Basic information

Entry
Database: PDB / ID: 3n53
TitleCrystal structure of a response regulator receiver modulated diguanylate cyclase from Pelobacter carbinolicus
ComponentsResponse regulator receiver modulated diguanylate cyclase
KeywordsTRANSCRIPTION / Response regulator / Diguanylate cyclase / Protein Structure Initiative II(PSI II) / NYSGXRC / Structural Genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


phosphorelay signal transduction system / ATP binding
Similarity search - Function
GAF domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...GAF domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Response regulator / Reverse transcriptase/Diguanylate cyclase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Response receiver sensor diguanylate cyclase, GAF domain-containing
Similarity search - Component
Biological speciesPelobacter carbinolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPalani, K. / Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a response regulator receiver modulated diguanylate cyclase from Pelobacter carbinolicus
Authors: Palani, K. / Zhang, Z. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: 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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver modulated diguanylate cyclase
B: Response regulator receiver modulated diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)33,0012
Polymers33,0012
Non-polymers00
Water79344
1
A: Response regulator receiver modulated diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)16,5001
Polymers16,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator receiver modulated diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)16,5001
Polymers16,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.004, 44.932, 88.681
Angle α, β, γ (deg.)90.00, 94.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Response regulator receiver modulated diguanylate cyclase


Mass: 16500.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pelobacter carbinolicus (bacteria) / Strain: DSM 2380/Gra Bd1 / Gene: Pcar_0634 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3A6W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium acetate, 0.1M Bis-Tris, 25% PEG 3350, pH 6.5, 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: Nov 7, 2009 / Details: MIRRORS
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→44.21 Å / Num. all: 13639 / Num. obs: 13639 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 37.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1310 / % possible all: 95.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NXO

1nxo


Resolution: 2.2→44.21 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 129766.7 / 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
Rfree0.286 675 5.1 %RANDOM
Rwork0.252 ---
all0.269 13633 --
obs0.252 13226 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.6717 Å2 / ksol: 0.36118 e/Å3
Displacement parametersBiso mean: 34.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.17 Å20 Å2-6.34 Å2
2---5.86 Å20 Å2
3----0.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→44.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 44 1780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.69
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 103 5.1 %
Rwork0.268 1905 -
obs-1310 87.8 %
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

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