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- PDB-4zmu: Dcsbis, a diguanylate cyclase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4zmu
TitleDcsbis, a diguanylate cyclase from Pseudomonas aeruginosa
Componentsdiguanylate cyclase
KeywordsLYASE / cell motilities / diguanyl cyclase / GGDEF domain / GAF 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
GGDEF domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.502 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 from Pseudomonas aeruginosa
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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: diguanylate cyclase
B: diguanylate cyclase
C: diguanylate cyclase
D: diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)153,5304
Polymers153,5304
Non-polymers00
Water2,468137
1
A: diguanylate cyclase
B: diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)76,7652
Polymers76,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-22 kcal/mol
Surface area27620 Å2
MethodPISA
2
C: diguanylate cyclase
D: diguanylate cyclase


Theoretical massNumber of molelcules
Total (without water)76,7652
Polymers76,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.609, 109.083, 111.850
Angle α, β, γ (deg.)90.00, 95.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
diguanylate cyclase /


Mass: 38382.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: PA2771 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9I072
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000, 0.1 M HEPES pH 7.5, 8% ethylene glycol

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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: May 10, 2010
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: 58687 / % possible obs: 96.6 % / Redundancy: 3.7 % / Rsym value: 0.069 / Net I/σ(I): 19.86
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.81 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.502→42.259 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 1999 3.41 %
Rwork0.1877 --
obs0.1896 58646 96.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.502→42.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10633 0 0 137 10770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910825
X-RAY DIFFRACTIONf_angle_d1.24614676
X-RAY DIFFRACTIONf_dihedral_angle_d16.6094112
X-RAY DIFFRACTIONf_chiral_restr0.0751660
X-RAY DIFFRACTIONf_plane_restr0.0051963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5018-2.56430.32621090.28293081X-RAY DIFFRACTION74
2.5643-2.63360.35321270.26773592X-RAY DIFFRACTION86
2.6336-2.71110.30811380.27023895X-RAY DIFFRACTION94
2.7111-2.79860.33981450.25294129X-RAY DIFFRACTION98
2.7986-2.89860.32481460.24874130X-RAY DIFFRACTION100
2.8986-3.01460.32881470.24624183X-RAY DIFFRACTION100
3.0146-3.15180.29011460.23134149X-RAY DIFFRACTION100
3.1518-3.31790.26361490.21854211X-RAY DIFFRACTION100
3.3179-3.52570.27491480.20184194X-RAY DIFFRACTION100
3.5257-3.79770.25451480.18824170X-RAY DIFFRACTION100
3.7977-4.17960.23811480.17014209X-RAY DIFFRACTION100
4.1796-4.78370.18251480.15214196X-RAY DIFFRACTION100
4.7837-6.02420.23091500.16964234X-RAY DIFFRACTION100
6.0242-42.26470.17771500.13344274X-RAY DIFFRACTION100

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