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- PDB-4zmm: GGDEF domain of Dcsbis complexed with c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 4zmm
TitleGGDEF domain of Dcsbis complexed with c-di-GMP
Componentsdiguanylate cyclase
KeywordsTRANSFERASE / cell motilities / diguanyl cyclase / GGDEF domain
Function / homology
Function and homology information


diguanylate cyclase activity / nucleotide binding
Similarity search - Function
Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain ...Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / GGDEF domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsChen, Y. / Liu, C. / Liu, S. / Chi, K. / Gu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program)2015CB150600 China
CitationJournal: To Be Published
Title: Crystal structure of Dcsbis GGDEF domain complexed with c-di-GMP
Authors: Chen, Y. / Liu, C. / Liu, S. / Chi, K. / Gu, L.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: diguanylate cyclase
B: diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9674
Polymers49,5862
Non-polymers1,3812
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint13 kcal/mol
Surface area16040 Å2
Unit cell
Length a, b, c (Å)93.275, 42.707, 106.372
Angle α, β, γ (deg.)90.00, 106.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein diguanylate cyclase


Mass: 24793.203 Da / Num. of mol.: 2 / Fragment: UNP residues 123-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2771 / Plasmid: pET 15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I072, diguanylate cyclase
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 39.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.5 M sodium citrate tribasic dehydrate, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 7, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13825 / % possible obs: 98.2 % / Redundancy: 3.4 % / Rsym value: 0.047 / Net I/σ(I): 46.34
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.6 % / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
SCALEPACKdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Full-length Dcsbis

Resolution: 2.503→37.618 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 683 5.02 %
Rwork0.2014 --
obs0.2038 13598 96.09 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.388 Å2 / ksol: 0.365 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-26.4166 Å2-0 Å28.6986 Å2
2---14.8767 Å20 Å2
3----11.5398 Å2
Refinement stepCycle: LAST / Resolution: 2.503→37.618 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2513 0 92 69 2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082651
X-RAY DIFFRACTIONf_angle_d1.3173605
X-RAY DIFFRACTIONf_dihedral_angle_d33.2021103
X-RAY DIFFRACTIONf_chiral_restr0.072409
X-RAY DIFFRACTIONf_plane_restr0.004463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5032-2.69640.32171490.2462483X-RAY DIFFRACTION93
2.6964-2.96770.29241380.22152536X-RAY DIFFRACTION97
2.9677-3.39690.24681210.20392628X-RAY DIFFRACTION98
3.3969-4.27870.22261430.17582665X-RAY DIFFRACTION99
4.2787-37.6220.23181320.20372603X-RAY DIFFRACTION94

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