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- PDB-3n3t: Crystal structure of putative diguanylate cyclase/phosphodiestera... -

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Basic information

Entry
Database: PDB / ID: 3n3t
TitleCrystal structure of putative diguanylate cyclase/phosphodiesterase complex with cyclic di-gmp
ComponentsPUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
KeywordsStructural Genomics / Unknown function / GGDEF & EAL DOMAINS / PSI-2 / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


nucleotide binding / membrane / metal ion binding
Similarity search - Function
EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Bacterial periplasmic substrate-binding proteins / GGDEF domain profile. ...EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Bacterial periplasmic substrate-binding proteins / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-C2E / Putative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains)
Similarity search - Component
Biological speciesTHIOBACILLUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsChang, C. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural insight into the mechanism of c-di-GMP hydrolysis by EAL domain phosphodiesterases.
Authors: Tchigvintsev, A. / Xu, X. / Singer, A. / Chang, C. / Brown, G. / Proudfoot, M. / Cui, H. / Flick, R. / Anderson, W.F. / Joachimiak, A. / Galperin, M.Y. / Savchenko, A. / Yakunin, A.F.
History
DepositionMay 20, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 16, 2010ID: 3II8
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
B: PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2669
Polymers65,7522
Non-polymers1,5137
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-59 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.560, 63.201, 173.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PUTATIVE DIGUANYLATE CYCLASE/PHOSPHODIESTERASE


Mass: 32876.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THIOBACILLUS DENITRIFICANS (bacteria) / Strain: ATCC 25259 / Gene: TBD_1265 / Plasmid: PET DERIVATIVE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) DERIVATIVE / References: UniProt: Q3SJE6
#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 / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M MAGNESIUM CHLORIDE, 25% PEG3350, 0.1M BIS-TRIS, 2.5MM CYCLIC DI-GMP, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 8, 2009
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 24452 / Num. obs: 24433 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 34.6
Reflection shellResolution: 2.35→2.37 Å / Redundancy: 7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 5.19 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→39.955 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.135 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R Free: 0.265
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25363 1239 5.1 %RANDOM
Rwork0.18403 ---
obs0.18757 23047 99.38 %-
all-24286 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.92 Å20 Å20 Å2
2---2.1 Å20 Å2
3----2.82 Å2
Refinement stepCycle: LAST / Resolution: 2.35→39.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 97 225 4322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214218
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9975744
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.585529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67223.177192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.08215696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5461546
X-RAY DIFFRACTIONr_chiral_restr0.0920.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213176
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9531.52612
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76624177
X-RAY DIFFRACTIONr_scbond_it2.90231606
X-RAY DIFFRACTIONr_scangle_it4.6514.51566
X-RAY DIFFRACTIONr_rigid_bond_restr1.50234218
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.351→2.412 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 93 -
Rwork0.2 1612 -
obs--97.1 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.1491-4.3838-0.41773.60770.35294.91780.2023-0.21480.3567-0.10290.115-0.2497-0.44780.4842-0.31720.0892-0.02070.02880.1206-0.01860.044616.2139.503333.9521
22.81-0.0521-1.68820.9165-0.33382.4758-0.11580.0639-0.0405-0.0070.07750.113-0.0394-0.16580.03830.0628-0.0017-0.01170.058-0.00730.0562-6.084939.643348.3394
34.46080.5175-0.7094.99491.60794.88970.07690.0381-0.25640.0629-0.1036-0.43560.00130.15390.02670.09020.003-0.01130.06130.03090.100610.41133.421338.9283
40.8189-0.21350.23341.7157-1.12792.1451-0.0212-0.04850.04770.1206-0.0612-0.1089-0.34250.19130.08240.0945-0.0309-0.01950.0295-0.00480.01885.376247.321454.6597
51.2394-0.16631.38640.6795-0.62733.51260.0188-0.0565-0.1271-0.0069-0.03060.12250.1674-0.13790.01180.04350.00010.01080.041-0.00740.0639-7.757632.234458.3616
617.60040.3437-11.674817.303-18.745227.58310.2662-0.60710.5367-0.3068-0.402-0.50490.17430.85540.13580.02750.0353-0.05020.1079-0.1480.28735.213928.232394.2143
74.2215-0.0011-0.01271.2247-0.68681.5314-0.0999-0.050.11080.16060.08690.02780.0189-0.06240.01310.0437-0.0062-0.00650.0947-0.01290.03689.829129.979798.5135
84.3192-3.4278-2.91347.22321.26578.17290.052-0.12420.50170.02630.1245-0.8316-0.52050.6918-0.17640.0497-0.084-0.00970.1825-0.03480.281328.613934.996193.5578
90.7531-0.28750.47551.38710.04051.74110.01970.0802-0.0857-0.0262-0.0096-0.06240.14560.0478-0.01020.0172-0.0092-0.00460.04830.01440.058314.046520.955586.8575
100.58920.05440.46350.6333-0.06652.5948-0.0493-0.15120.1008-0.02060.00240.0624-0.1494-0.19340.04690.01430.0198-0.01720.0696-0.01170.05762.644936.967891.5197
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A489 - 503
2X-RAY DIFFRACTION2A504 - 527
3X-RAY DIFFRACTION3A528 - 547
4X-RAY DIFFRACTION4A548 - 663
5X-RAY DIFFRACTION5A664 - 743
6X-RAY DIFFRACTION6B489 - 503
7X-RAY DIFFRACTION7B504 - 527
8X-RAY DIFFRACTION8B528 - 547
9X-RAY DIFFRACTION9B548 - 663
10X-RAY DIFFRACTION10B664 - 743

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