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- PDB-3ign: Crystal Structure of the GGDEF domain from Marinobacter aquaeolei... -

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Basic information

Entry
Database: PDB / ID: 3ign
TitleCrystal Structure of the GGDEF domain from Marinobacter aquaeolei diguanylate cyclase complexed with c-di-GMP - Northeast Structural Genomics Consortium Target MqR89a
ComponentsDiguanylate cyclase
KeywordsTRANSFERASE / Diguanylate cyclase / GGDEF domain / A1U3W3_MARAV / NESG / MqR89a / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


diguanylate cyclase / nucleotide binding
Similarity search - Function
PAS fold-4 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain ...PAS fold-4 / PAS fold / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / diguanylate cyclase
Similarity search - Component
Biological speciesMarinobacter aquaeolei VT8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsVorobiev, S. / Neely, H. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. ...Vorobiev, S. / Neely, H. / Seetharaman, J. / Wang, H. / Foote, E.L. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product.
Authors: Vorobiev, S.M. / Neely, H. / Yu, B. / Seetharaman, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionJul 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diguanylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8453
Polymers20,4641
Non-polymers1,3812
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.229, 59.229, 118.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Diguanylate cyclase


Mass: 20463.838 Da / Num. of mol.: 1 / Fragment: GGDEF domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter aquaeolei VT8 (bacteria) / Gene: Maqu_2607 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: A1U3W3, 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.: 168 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% MPD, 0.1M magnesium acetate, 0.1M cacodylate, 3 mM GTP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 35738 / Num. obs: 35667 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.4 % / Biso Wilson estimate: 29.14 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 78.6
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 14.2 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 6 / Num. unique all: 1801 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SnBphasing
RESOLVEmodel building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→32.938 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 23.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1810 5.09 %random
Rwork0.195 ---
obs0.1973 35531 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.588 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1686 Å20 Å20 Å2
2---0.1686 Å20 Å2
3---0.3373 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.83→32.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1301 0 92 168 1561
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_deg1.5
X-RAY DIFFRACTIONf_dihedral_angle_d21.3
X-RAY DIFFRACTIONf_improper_angle_d0.83
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.87920.30091360.19192602X-RAY DIFFRACTION100
1.8792-1.93450.25271310.192609X-RAY DIFFRACTION100
1.9345-1.99690.22981340.18552641X-RAY DIFFRACTION100
1.9969-2.06820.22241330.16942593X-RAY DIFFRACTION100
2.0682-2.1510.28621460.17842578X-RAY DIFFRACTION100
2.151-2.24890.26241570.17992594X-RAY DIFFRACTION100
2.2489-2.36740.21891650.19192584X-RAY DIFFRACTION100
2.3674-2.51570.24871180.18482585X-RAY DIFFRACTION100
2.5157-2.70990.25891540.21442602X-RAY DIFFRACTION100
2.7099-2.98240.27121590.20022572X-RAY DIFFRACTION100
2.9824-3.41360.22821140.18472616X-RAY DIFFRACTION100
3.4136-4.29930.1991310.17322596X-RAY DIFFRACTION100
4.2993-32.94340.21891320.21322549X-RAY DIFFRACTION97

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