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- PDB-6ij2: Crystal structure of a standalone versatile EAL protein from Vibr... -

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Basic information

Entry
Database: PDB / ID: 6ij2
TitleCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 5'-pGpG bound form
Components
  • EAL domain protein
  • RNA (5'-R(P*GP*G)-3')
KeywordsHYDROLASE / cyclic dinucleotide phosphodiesterase / nucleotide binding
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase activity / nucleotide binding / metal ion binding
Similarity search - Function
: / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain
Similarity search - Domain/homology
RNA / EAL domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYadav, M. / Pal, K. / Sen, U.
CitationJournal: Biochem.J. / Year: 2019
Title: Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.
Authors: Yadav, M. / Pal, K. / Sen, U.
History
DepositionOct 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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
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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EAL domain protein
E: RNA (5'-R(P*GP*G)-3')
B: EAL domain protein
F: RNA (5'-R(P*GP*G)-3')
C: EAL domain protein
G: RNA (5'-R(P*GP*G)-3')
D: EAL domain protein
H: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,32324
Polymers118,6828
Non-polymers64116
Water11,043613
1
A: EAL domain protein
E: RNA (5'-R(P*GP*G)-3')
D: EAL domain protein
H: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66212
Polymers59,3414
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-138 kcal/mol
Surface area19920 Å2
MethodPISA
2
B: EAL domain protein
F: RNA (5'-R(P*GP*G)-3')
C: EAL domain protein
G: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,66212
Polymers59,3414
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-136 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.483, 42.711, 158.470
Angle α, β, γ (deg.)90.000, 94.940, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
EAL domain protein


Mass: 29025.090 Da / Num. of mol.: 4 / Mutation: C15S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A1247 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AJ04
#2: RNA chain
RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 613 / 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: 2.14 Å3/Da / Density % sol: 42.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 4000, sodium acetate, ammonium acetate / PH range: 3.6-5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.7→52.63 Å / Num. obs: 106944 / % possible obs: 98.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.024 / Rrim(I) all: 0.045 / Net I/σ(I): 13.8 / Num. measured all: 361603
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.733.40.652300.8820.3840.71599.5
9.31-52.632.90.0297090.9980.0230.03796.2

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFX

3gfx


Resolution: 1.7→51.511 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.67
RfactorNum. reflection% reflection
Rfree0.2202 5277 4.95 %
Rwork0.1818 --
obs0.1837 106643 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 242.01 Å2 / Biso mean: 44.8198 Å2 / Biso min: 16.9 Å2
Refinement stepCycle: final / Resolution: 1.7→51.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7556 188 16 613 8373
Biso mean--60.95 46.49 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0188018
X-RAY DIFFRACTIONf_angle_d0.79710744
X-RAY DIFFRACTIONf_chiral_restr0.0551184
X-RAY DIFFRACTIONf_plane_restr0.0041368
X-RAY DIFFRACTIONf_dihedral_angle_d17.2344724
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.36091900.31353300349099
1.7193-1.73950.33531660.29733390355699
1.7395-1.76080.31121750.2763404357999
1.7608-1.78310.33791840.25723376356099
1.7831-1.80650.26691690.24193340350999
1.8065-1.83130.27181790.22813347352699
1.8313-1.85740.28051870.23243435362299
1.8574-1.88520.25861580.21433391354999
1.8852-1.91460.26331900.20693350354099
1.9146-1.9460.25081790.20543380355998
1.946-1.97960.24521860.20513356354298
1.9796-2.01560.26441880.20133348353698
2.0156-2.05430.23081610.19813383354499
2.0543-2.09630.23871680.19123368353698
2.0963-2.14180.23621720.18813423359599
2.1418-2.19170.22351750.18183324349998
2.1917-2.24650.21691750.17733405358098
2.2465-2.30720.21381650.18043329349498
2.3072-2.37510.23951960.17983381357797
2.3751-2.45180.20921800.17893327350798
2.4518-2.53940.24281930.18123344353798
2.5394-2.64110.20191610.1823377353897
2.6411-2.76130.21871760.18593223339995
2.7613-2.90680.2181490.18033168331791
2.9068-3.08890.22311800.17993401358198
3.0889-3.32740.19231740.16333479365399
3.3274-3.66210.20591750.163434563631100
3.6621-4.19190.19641880.1573471365999
4.1919-5.28050.19181490.15413556370599
5.2805-51.53510.21511890.2013534372398
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)
12.5599-0.24970.73122.332-0.04443.38350.00390.98440.0222-0.59250.0092-0.06340.1351-0.0652-0.01380.3131-0.0042-0.00910.652-0.05590.3158-42.62116.8504-71.1158
24.0793-1.4570.29095.94252.73295.9118-0.00050.8681.139-0.86760.2177-0.44-0.84060.3234-0.24050.3788-0.01810.00210.58370.15840.4987-42.171716.9798-68.2273
33.56960.24390.73361.6508-0.24771.84230.01650.40270.2774-0.1267-0.14290.0046-0.10660.00960.12420.19120.02130.01690.3743-0.00420.2592-36.124311.611-56.9729
48.1186-1.54773.80165.83671.94226.33240.0767-1.0503-1.8880.93220.27350.0451.3524-0.8912-0.41810.6059-0.0853-0.03560.68050.13260.7645-46.8099-6.49-53.7687
53.3070.00692.27322.0687-0.30468.4771-0.07310.9935-0.2297-0.1770.1743-0.2493-0.08360.70970.16690.4644-0.1037-0.01940.8495-0.14730.4198-35.29673.7056-66.5173
63.0002-0.0086-0.43682.0299-0.21384.90170.092-0.62780.28650.41890.03770.0715-0.2896-0.047-0.07240.21860.01340.01180.3380.01450.2557-24.19186.2797-8.8886
72.9546-0.09750.90611.33590.13482.23320.0031-0.21480.16370.0673-0.05960.0262-0.05390.05160.03110.1427-0.00620.03520.17680.03120.195-29.53548.408-22.3228
82.3401-0.59360.53560.3240.32923.13530.0269-0.5665-0.12030.040.11850.1517-0.0555-0.3376-0.0230.332-0.0103-0.00570.42140.07850.3089-31.40470.878-13.309
94.31451.201-0.98342.87780.03453.22520.1873-0.5806-0.080.5802-0.03190.11110.0072-0.2025-0.10940.22440.0147-0.00770.41150.04980.3178-68.004815.9264-16.6196
104.06020.1247-0.73471.9022-0.43691.72150.0077-0.1287-0.04670.1149-0.00060.0960.0167-0.1367-0.01730.15480.0062-0.01420.1941-0.00530.186-55.573417.0194-27.731
115.2574-0.0712-1.56060.4512-0.96564.13460.1086-1.03560.23150.4914-0.155-0.0571-0.0276-0.076-0.0830.43510.01990.00450.5068-0.07050.4123-58.955322.8274-17.3083
124.7544-0.7845-0.16943.16260.07874.45250.04530.6787-0.1887-0.53980.0003-0.05750.00310.1357-0.05910.2511-0.0295-0.0070.5589-0.01510.32331.433118.6115-61.842
134.24590.3564-0.19241.95670.25841.4507-0.02560.2851-0.1394-0.0998-0.0065-0.03490.00330.07690.00790.18950.007-0.02580.2950.02190.2103-11.088918.6574-50.6675
142.74640.2093-0.83640.70831.07882.26570.00071.10110.543-0.5209-0.0720.2567-0.1227-0.06360.00270.4017-0.01230.02980.76430.12040.4573-7.959125.4064-60.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 85 )A22 - 85
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 108 )A86 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 245 )A109 - 245
4X-RAY DIFFRACTION4chain 'A' and (resid 246 through 257 )A246 - 257
5X-RAY DIFFRACTION5chain 'E' and (resid 503 through 504 )E503 - 504
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 107 )B22 - 107
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 257 )B108 - 257
8X-RAY DIFFRACTION8chain 'F' and (resid 503 through 504 )F503 - 504
9X-RAY DIFFRACTION9chain 'C' and (resid 22 through 117 )C22 - 117
10X-RAY DIFFRACTION10chain 'C' and (resid 118 through 257 )C118 - 257
11X-RAY DIFFRACTION11chain 'G' and (resid 503 through 504 )G503 - 504
12X-RAY DIFFRACTION12chain 'D' and (resid 22 through 117 )D22 - 117
13X-RAY DIFFRACTION13chain 'D' and (resid 118 through 257 )D118 - 257
14X-RAY DIFFRACTION14chain 'H' and (resid 503 through 504 )H503 - 504

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