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- PDB-3u2e: EAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++ -

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Basic information

Entry
Database: PDB / ID: 3u2e
TitleEAL domain of phosphodiesterase PdeA in complex with 5'-pGpG and Mg++
Components
  • GGDEF family protein
  • RNA (5'-R(P*GP*G)-3')
Keywordslyase/RNA / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GGDEF / EAL / c-diGMP / lyase-RNA complex
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / PdeA-like PAS domain / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase ...: / PdeA-like PAS domain / EAL domain / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
RNA / GGDEF family protein
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Massa, C. / Schirmer, T. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: EAL domain from Caulobacter crescentus in complex with 5'-pGpG and Mg++
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Massa, C. / Schirmer, T. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Structure summary
Revision 1.2Oct 12, 2016Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GGDEF family protein
B: GGDEF family protein
C: RNA (5'-R(P*GP*G)-3')
D: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,92910
Polymers58,7844
Non-polymers1466
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-92 kcal/mol
Surface area21990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.144, 75.154, 129.066
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 GGDEF family protein


Mass: 28746.342 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_3396 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q9A310
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsACCORDING TO PROTEOLYSIS THE PROTEIN WAS DEGRADED AND ONLY PART OF THE PROTEIN WAS CRYSTALLIZED ...ACCORDING TO PROTEOLYSIS THE PROTEIN WAS DEGRADED AND ONLY PART OF THE PROTEIN WAS CRYSTALLIZED WHICH IS SEEN IN THE CRYSTAL STRUCTURE

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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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Magnesium chloride hexahydrate, 20% w/v PEG3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2011 / Details: BE
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. all: 51468 / Num. obs: 51468 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.76
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 5.02 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3S83

3s83


Resolution: 2.32→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.74 / SU ML: 0.15 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23737 1333 5 %RANDOM
Rwork0.18927 ---
obs0.19175 25068 100 %-
all-25068 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.511 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--3.08 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.32→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3917 94 6 154 4171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194111
X-RAY DIFFRACTIONr_bond_other_d0.0010.022764
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.9795599
X-RAY DIFFRACTIONr_angle_other_deg0.97136713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9595517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54623.2175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23915609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4051538
X-RAY DIFFRACTIONr_chiral_restr0.1090.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214584
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02842
LS refinement shellResolution: 2.323→2.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 68 -
Rwork0.261 1569 -
obs--89.5 %
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)
12.2893-0.19770.69061.9342-0.35512.10510.15480.126-0.5034-0.0283-0.09910.14620.1666-0.1458-0.05570.03350.0132-0.02740.0868-0.02580.13217.1738-4.685750.936
21.9195-0.0777-0.41250.82150.03642.1283-0.09320.0632-0.1670.01660.0249-0.10150.21410.39310.06830.04470.0487-0.00770.1261-0.00260.052433.451-2.296556.2099
32.2993-0.81691.35511.0262-0.7763.5203-0.2166-0.34710.04050.25870.15150.0342-0.4041-0.25780.06510.12050.0638-0.01080.0966-0.00920.015121.26277.87167.1796
41.0738-0.09110.61482.1727-0.36671.81960.0638-0.0795-0.1617-0.0164-0.0656-0.19930.21750.12230.00180.0395-0.0076-0.01370.08090.03420.077446.7783-9.826104.3591
51.27130.4595-0.44711.0027-0.61721.7581-0.009-0.12710.08720.01040.09370.12670.0987-0.3162-0.08470.0172-0.0208-0.01370.12750.03040.051730.3656-2.6934103.1087
61.3755-0.07920.61911.1359-0.79582.1828-0.05810.08150.1551-0.1828-0.0223-0.1193-0.03130.04470.08040.0544-0.01590.00140.05940.03680.059740.34425.918489.351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A287 - 375
2X-RAY DIFFRACTION2A376 - 443
3X-RAY DIFFRACTION3A444 - 546
4X-RAY DIFFRACTION4B286 - 359
5X-RAY DIFFRACTION5B360 - 441
6X-RAY DIFFRACTION6B442 - 540

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