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- PDB-2r6o: Crystal structure of putative diguanylate cyclase/phosphodiestera... -

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Basic information

Entry
Database: PDB / ID: 2r6o
TitleCrystal structure of putative diguanylate cyclase/phosphodiesterase from Thiobacillus denitrificans
ComponentsPutative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains)
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / diguanylate cyclase / GGDEF and EAL domains / Thiobacillus denitrificans / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / TRANSFERASE
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 profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Bacterial periplasmic substrate-binding proteins ...: / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains)
Similarity search - Component
Biological speciesThiobacillus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / 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
DepositionSep 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains)
B: Putative diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9328
Polymers65,7522
Non-polymers1796
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.051, 63.141, 173.282
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 (GGDEF & EAL domains)


Mass: 32876.148 Da / Num. of mol.: 2 / Fragment: Residues 487-758
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M MgCl2, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97857 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 13, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 51848 / Num. obs: 50452 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 39.67
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.26 / Num. unique all: 4585 / % possible all: 90.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→27.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.001 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21756 2554 5.1 %RANDOM
Rwork0.18829 ---
all0.1898 47788 --
obs0.1898 47788 97.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å20 Å2
2---0.57 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3835 0 6 378 4219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224039
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9685510
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1525540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25923.487195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53215697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3691545
X-RAY DIFFRACTIONr_chiral_restr0.0860.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023098
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21840
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2970.22802
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2308
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2820.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.52639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14524093
X-RAY DIFFRACTIONr_scbond_it2.01431573
X-RAY DIFFRACTIONr_scangle_it3.0544.51397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 148 -
Rwork0.227 3164 -
obs--88.51 %
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)
115.64266.2148-2.22856.7173-0.7498.39430.33650.48520.52320.0059-0.00310.3677-0.7044-1.1463-0.3335-0.04040.10270.04110.03680.0293-0.168133.703939.701952.8224
25.1684-0.2991-2.6091.08460.74272.7535-0.00740.10790.0150.1987-0.0032-0.2018-0.01270.14810.0105-0.0750.0165-0.0234-0.07770.0128-0.044356.037439.765738.5154
34.01020.02451.45117.3113-0.56055.56910.1086-0.2581-0.1551-0.2396-0.09590.23820.1586-0.1924-0.01270.015-0.0129-0.0161-0.07280.0046-0.027839.259733.5947.8845
40.48780.1337-0.05231.65460.49552.0621-0.0030.0466-0.0036-0.0675-0.05560.1305-0.3132-0.19720.0586-0.00780.0479-0.0164-0.0838-0.003-0.044344.573347.578732.2183
51.16190.00331.07752.14530.67063.83740.01850.093-0.02670.0188-0.0149-0.19280.26650.3065-0.0035-0.05440.03510.0093-0.03730.013-0.03257.704832.61228.6319
619.60973.2553-7.762222.436421.826656.10730.36040.26061.4630.86910.1595-0.0254-0.6439-0.9586-0.5199-0.20170.0875-0.1051-0.13860.05640.208815.620827.8723-7.5893
78.62061.1754-1.01112.346-0.0053.9373-0.02550.43360.141-0.05360.06550.1361-0.15040.3558-0.04-0.1093-0.0098-0.0223-0.01480.0054-0.149640.099329.9539-11.2918
829.75046.967-7.746619.666-21.711336.8399-0.63063.40631.55510.38810.6841.1258-1.9765-2.6037-0.05340.01360.0196-0.1137-0.0119-0.03450.227819.155631.2594-9.3168
91.1880.07820.73221.4850.09961.4284-0.0047-0.0009-0.07160.0907-0.03430.11930.0518-0.07490.039-0.1172-0.00160.0117-0.0407-0.0272-0.036736.101620.77850.5506
101.1750.16751.31411.08910.91954.1964-0.22110.31340.1327-0.1320.09490.0193-0.590.4710.1262-0.0129-0.0797-0.01810.01870.0471-0.05347.040937.0098-3.9865
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA489 - 50325 - 39
2X-RAY DIFFRACTION2AA504 - 52740 - 63
3X-RAY DIFFRACTION3AA528 - 54764 - 83
4X-RAY DIFFRACTION4AA548 - 66384 - 199
5X-RAY DIFFRACTION5AA664 - 743200 - 279
6X-RAY DIFFRACTION6BB489 - 50325 - 39
7X-RAY DIFFRACTION7BB504 - 52740 - 63
8X-RAY DIFFRACTION8BB528 - 54764 - 83
9X-RAY DIFFRACTION9BB548 - 66384 - 199
10X-RAY DIFFRACTION10BB664 - 743200 - 279

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