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- PDB-6ih7: Crystal structure of a standalone versatile EAL protein from Vibr... -

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Basic information

Entry
Database: PDB / ID: 6ih7
TitleCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - 3',3'-cGAMP bound form
Componentscyclic di nucleotide phoshodiesterase
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
Chem-4BW / EAL domain-containing protein
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionSep 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: cyclic di nucleotide phoshodiesterase
A: cyclic di nucleotide phoshodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5598
Polymers58,0502
Non-polymers1,5096
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area20940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.899, 42.600, 73.330
Angle α, β, γ (deg.)90.000, 94.910, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein cyclic di nucleotide phoshodiesterase


Mass: 29025.090 Da / Num. of mol.: 2 / 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, cyclic-guanylate-specific phosphodiesterase
#2: Chemical ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium acetate, tris / PH range: 8-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.25→55.974 Å / Num. obs: 22200 / % possible obs: 95.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 35.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Rrim(I) all: 0.051 / Net I/σ(I): 15.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.25-2.323.20.16919510.9760.1150.20593.3
9-55.9730.0373780.9950.0250.04592.6

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Processing

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

3gfx


Resolution: 2.25→55.974 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.62
RfactorNum. reflection% reflection
Rfree0.2397 1040 4.7 %
Rwork0.1813 --
obs0.1842 22141 94.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 178.12 Å2 / Biso mean: 64.6215 Å2 / Biso min: 21.83 Å2
Refinement stepCycle: final / Resolution: 2.25→55.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 94 61 3944
Biso mean--51.58 48.98 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013987
X-RAY DIFFRACTIONf_angle_d0.9725384
X-RAY DIFFRACTIONf_chiral_restr0.052589
X-RAY DIFFRACTIONf_plane_restr0.006686
X-RAY DIFFRACTIONf_dihedral_angle_d18.7872353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2501-2.36870.28011290.22792936306592
2.3687-2.51710.26541270.2092941306893
2.5171-2.71140.30711370.20872985312294
2.7114-2.98430.2531490.19272980312995
2.9843-3.41610.24951590.19343043320295
3.4161-4.30360.20681700.16493089325996
4.3036-55.99130.23461690.16463127329695
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)
12.5416-0.46772.13092.77640.39943.75550.22370.20350.0843-0.0421-0.05950.6634-0.2962-1.5103-0.18080.45760.23150.01130.83580.08680.377-32.3974-2.269325.8262
29.0999-1.17590.37536.7133.13233.5611-0.1909-0.2192-0.81850.31250.04531.1271.0387-1.1260.10060.4228-0.0890.01760.86470.03190.4527-33.9355-12.36523.2922
36.0914-1.51431.44236.8775-2.140.81830.37050.1287-0.6242-0.0915-0.01290.54361.3016-0.8847-0.2960.6633-0.2625-0.02210.6518-0.07480.3733-29.1833-17.974425.7719
49.2197-1.06650.89117.03721.35431.4622-0.026-0.3845-0.0130.804-0.06220.00091.0307-1.59860.26130.6537-0.05370.04690.35070.03960.2703-23.072-12.749434.5977
52.31040.86370.86823.5868-1.23524.52860.0974-0.03-0.01690.2431-0.2586-0.0204-0.05740.09310.14520.49020.08680.04060.17330.0110.261-13.3298-5.578836.9401
68.24990.53416.68363.47713.08348.1077-0.90880.51781.3357-0.35410.56190.1389-1.53590.04470.27480.78550.1621-0.06950.33930.10210.3776-19.88747.166923.4734
75.0514-0.7298-2.84994.47080.74554.7339-0.3153-0.5288-0.24510.35720.2190.77851.1437-0.66670.13930.5852-0.21660.00840.65760.09820.3342-24.5176-23.103968.6217
85.6753-2.1296-2.636.41081.1511.2298-0.06110.12610.5045-0.4713-0.29721.5838-0.1111-1.41380.53420.4115-0.22-0.20791.86240.06570.8821-40.7707-17.943462.2974
95.25672.51323.33747.80811.89517.6438-0.8796-0.39290.36330.08950.1491.2913-0.5372-1.40820.6810.48370.05450.061.09280.00390.3557-31.4343-14.868972.6602
103.65351.6639-2.4017.88753.57515.1463-0.2275-0.09290.4356-0.62980.33951.361-1.1761-0.92280.14970.46530.1504-0.03880.72150.06640.4504-27.161-9.017766.6018
115.8340.9067-1.77437.0902-1.51851.51060.0663-0.43290.4877-0.2256-0.260.5469-0.7257-1.1669-0.04930.35160.139-0.05790.6131-0.11810.3132-25.446-7.875668.3586
127.81571.3279-5.35056.6509-3.14354.83850.79670.42191.2966-0.1488-0.2844-0.1157-2.4322-1.3896-0.68531.20490.1560.24810.6169-0.05190.4897-22.9181-0.561761.9021
137.47841.6702-2.02113.86983.65675.39940.05990.08520.27070.04710.2425-0.0933-0.5422-1.2848-0.29090.61780.09330.04680.3040.0970.2721-20.917-11.907856.4108
142.3372-0.0319-0.17011.42291.11791.12050.33460.0292-0.044-0.3542-0.31230.06460.5376-0.44320.00040.81160.0065-0.06760.2735-0.01660.2714-16.3987-16.600851.7059
152.6377-0.17690.31696.522-2.83541.27750.2205-0.01810.02050.0089-0.4989-0.00120.83690.5180.34340.6593-0.04930.02170.21540.03550.2778-10.4644-18.158150.7152
164.22130.1482-3.33230.94740.23732.84790.2479-0.5641-0.4709-0.072-0.246-0.01031.28340.5189-0.0190.84090.1618-0.00880.31910.06690.305-9.7111-27.079856.7485
176.16863.6348-4.51162.5836-1.35527.2957-0.3233-0.4644-1.13170.20240.59850.22191.49050.10061.09261.2281-0.214-0.01420.37030.35760.2795-15.7851-31.733768.054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 67 )B21 - 67
2X-RAY DIFFRACTION2chain 'B' and (resid 68 through 107 )B68 - 107
3X-RAY DIFFRACTION3chain 'B' and (resid 108 through 151 )B108 - 151
4X-RAY DIFFRACTION4chain 'B' and (resid 152 through 166 )B152 - 166
5X-RAY DIFFRACTION5chain 'B' and (resid 167 through 235 )B167 - 235
6X-RAY DIFFRACTION6chain 'B' and (resid 236 through 257 )B236 - 257
7X-RAY DIFFRACTION7chain 'A' and (resid 21 through 55 )A21 - 55
8X-RAY DIFFRACTION8chain 'A' and (resid 56 through 67 )A56 - 67
9X-RAY DIFFRACTION9chain 'A' and (resid 68 through 86 )A68 - 86
10X-RAY DIFFRACTION10chain 'A' and (resid 87 through 107 )A87 - 107
11X-RAY DIFFRACTION11chain 'A' and (resid 108 through 138 )A108 - 138
12X-RAY DIFFRACTION12chain 'A' and (resid 139 through 151 )A139 - 151
13X-RAY DIFFRACTION13chain 'A' and (resid 152 through 166 )A152 - 166
14X-RAY DIFFRACTION14chain 'A' and (resid 167 through 191 )A167 - 191
15X-RAY DIFFRACTION15chain 'A' and (resid 192 through 219 )A192 - 219
16X-RAY DIFFRACTION16chain 'A' and (resid 220 through 238 )A220 - 238
17X-RAY DIFFRACTION17chain 'A' and (resid 239 through 257 )A239 - 257

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