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- PDB-6k6t: Crystal structure of a standalone versatile EAL protein from Vibr... -

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Basic information

Entry
Database: PDB / ID: 6k6t
TitleCrystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form
ComponentsEAL domain protein
KeywordsHYDROLASE / cyclic dinucleotide phosphodiesterase / nucleotide binding
Function / homologyPutative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / nucleotide binding / metal ion binding / Chem-C2I / EAL domain-containing protein
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYadav, M. / Pal, K. / Sen, U.
CitationJournal: To Be Published
Title: Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-IMP bound form
Authors: Yadav, M. / Pal, K. / Sen, U.
History
DepositionJun 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EAL domain protein
B: EAL domain protein
C: EAL domain protein
D: EAL domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,06316
Polymers116,1004
Non-polymers2,96212
Water7,855436
1
A: EAL domain protein
D: EAL domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5318
Polymers58,0502
Non-polymers1,4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-39 kcal/mol
Surface area20330 Å2
MethodPISA
2
B: EAL domain protein
hetero molecules

C: EAL domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5318
Polymers58,0502
Non-polymers1,4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.450, 42.540, 155.040
Angle α, β, γ (deg.)90.000, 94.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 21 - 257 / Label seq-ID: 21 - 257

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

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Components

#1: Protein
EAL domain protein / EAL domain phosphodiesterase


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: pET 28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3AJ04, phosphodiesterase I
#2: Chemical
ChemComp-C2I / 9-[(1R,6R,8R,9S,10R,15S,17R,18S)-3,9,12,18-tetrakis(oxidanyl)-3,12-bis(oxidanylidene)-17-(6-oxidanylidene-3H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-3H-purin-6-one


Mass: 660.381 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22N8O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4000
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→51.51 Å / Num. obs: 47970 / % possible obs: 97.8 % / Redundancy: 3.1 % / Biso Wilson estimate: 26.39 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.107 / Rrim(I) all: 0.194 / Net I/σ(I): 4.1 / Num. measured all: 148871 / Scaling rejects: 64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.273.10.6471264840640.680.4260.7771.696.1
9.07-51.512.90.10221807420.9820.070.1257.196.3

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFX

3gfx


Resolution: 2.2→51.114 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.65
RfactorNum. reflection% reflection
Rfree0.2519 1990 4.16 %
Rwork0.197 --
obs0.1994 47885 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.06 Å2 / Biso mean: 44.8521 Å2 / Biso min: 16.61 Å2
Refinement stepCycle: final / Resolution: 2.2→51.114 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7576 0 184 436 8196
Biso mean--34.16 38.36 -
Num. residues----948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0157976
X-RAY DIFFRACTIONf_angle_d1.28510756
X-RAY DIFFRACTIONf_chiral_restr0.071176
X-RAY DIFFRACTIONf_plane_restr0.0081372
X-RAY DIFFRACTIONf_dihedral_angle_d18.1624660
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4612X-RAY DIFFRACTION20.634TORSIONAL
12B4612X-RAY DIFFRACTION20.634TORSIONAL
13C4612X-RAY DIFFRACTION20.634TORSIONAL
14D4612X-RAY DIFFRACTION20.634TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.2550.35831400.30763202334295
2.255-2.3160.32331290.27293186331596
2.316-2.38420.29861450.25043231337696
2.3842-2.46110.27671330.23733229336296
2.4611-2.54910.31541430.22753214335796
2.5491-2.65110.29221410.22243276341797
2.6511-2.77180.2791350.22093236337197
2.7718-2.91790.27911490.20883262341197
2.9179-3.10070.30361500.20753278342898
3.1007-3.34010.23291370.18563304344198
3.3401-3.67610.21531480.17763326347498
3.6761-4.20780.18761510.16033342349398
4.2078-5.30050.241410.15583394353598
5.3005-51.12740.22431480.1853415356397
Refinement TLS params.Method: refined / Origin x: -15.1106 Å / Origin y: -11.0933 Å / Origin z: -38.5939 Å
111213212223313233
T0.1988 Å20.0524 Å2-0.0178 Å2-0.1632 Å2-0.0028 Å2--0.264 Å2
L1.2742 °20.2865 °20.0662 °2-0.2864 °20.0574 °2--0.0925 °2
S0.0229 Å °0.0786 Å °0.0094 Å °-0.0212 Å °-0.0217 Å °-0.0084 Å °-0.0174 Å °0.0293 Å °0.0032 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA21 - 257
2X-RAY DIFFRACTION1allA501 - 602
3X-RAY DIFFRACTION1allB21 - 257
4X-RAY DIFFRACTION1allB501 - 602
5X-RAY DIFFRACTION1allC21 - 257
6X-RAY DIFFRACTION1allC501 - 602
7X-RAY DIFFRACTION1allD21 - 257
8X-RAY DIFFRACTION1allD501 - 602
9X-RAY DIFFRACTION1allS1 - 436

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