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- PDB-2w27: CRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN ... -

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Basic information

Entry
Database: PDB / ID: 2w27
TitleCRYSTAL STRUCTURE OF THE BACILLUS SUBTILIS YKUI PROTEIN, WITH AN EAL DOMAIN, IN COMPLEX WITH SUBSTRATE C-DI-GMP AND CALCIUM
ComponentsYKUI PROTEIN
KeywordsSIGNALING PROTEIN / PROTEIN STRUCTURE INITIATIVE / STRUCTURAL GENOMICS / PSI / MCSG / EAL DOMAIN / YKUI PROTEIN / CYCLIC DI-GMP
Function / homology
Function and homology information


YkuI, C-terminal / EAL-domain associated signalling protein domain / EAL domain / Periplasmic sensor-like domain superfamily / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain ...YkuI, C-terminal / EAL-domain associated signalling protein domain / EAL domain / Periplasmic sensor-like domain superfamily / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / PAS domain / Beta-Lactamase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Uncharacterized EAL-domain containing protein YkuI
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPadavattan, S. / AndERSON, W.F. / Schirmer, T.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Crystal Structures of Ykui and its Complex with Second Messenger C-Di-Gmp Suggests Catalytic Mechanism of Phosphodiester Bond Cleavage by Eal Domains.
Authors: Minasov, G. / Padavattan, S. / Shuvalova, L. / Brunzelle, J.S. / Miller, D.J. / Basle, A. / Massa, C. / Collart, F.R. / Schirmer, T. / Anderson, W.F.
History
DepositionOct 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 30, 2019Group: Advisory / Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.method
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YKUI PROTEIN
B: YKUI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0358
Polymers101,5022
Non-polymers1,5336
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-23.6 kcal/mol
Surface area43600 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.167, 124.521, 168.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUGLYGLYAA2 - 3626 - 60
211LEULEUGLYGLYBB2 - 3626 - 60
121ILEILEGLUGLUAA38 - 5862 - 82
221ILEILEGLUGLUBB38 - 5862 - 82
131TYRTYRASNASNAA60 - 6684 - 90
231TYRTYRASNASNBB60 - 6684 - 90
141ILEILEILEILEAA68 - 11492 - 138
241ILEILEILEILEBB68 - 11492 - 138
151LEULEUGLUGLUAA116 - 125140 - 149
251LEULEUGLUGLUBB116 - 125140 - 149
161ALAALASERSERAA204 - 237228 - 261
261ALAALASERSERBB204 - 237228 - 261
171THRTHRLEULEUAA239 - 241263 - 265
271THRTHRLEULEUBB239 - 241263 - 265
181ARGARGLYSLYSAA243 - 262267 - 286
281ARGARGLYSLYSBB243 - 262267 - 286
112LYSLYSARGARGAA264 - 287288 - 311
212LYSLYSARGARGBB264 - 287288 - 311
122TYRTYRTHRTHRAA313 - 323337 - 347
222TYRTYRTHRTHRBB313 - 323337 - 347
132LYSLYSPROPROAA342 - 384366 - 408
232LYSLYSPROPROBB342 - 384366 - 408
142ASPASPLEULEUAA386 - 391410 - 415
242ASPASPLEULEUBB386 - 391410 - 415
113HISHISTYRTYRAA126 - 136150 - 160
213HISHISTYRTYRBB126 - 136150 - 160
123METMETASPASPAA138 - 152162 - 176
223METMETASPASPBB138 - 152162 - 176
133LEULEUALAALAAA166 - 178190 - 202
233LEULEUALAALABB166 - 178190 - 202
143ALAALAGLYGLYAA199 - 203223 - 227
243ALAALAGLYGLYBB199 - 203223 - 227
114PHEPHEARGARGAA297 - 311321 - 335
214PHEPHEARGARGBB297 - 311321 - 335
124VALVALGLUGLUAA326 - 332350 - 356
224VALVALGLUGLUBB326 - 332350 - 356
134ILEILETYRTYRAA334 - 335358 - 359
234ILEILETYRTYRBB334 - 335358 - 359
1445GP5GPCACAAC - E501 - 503
2445GP5GPCACABF - H501 - 503

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein YKUI PROTEIN


Mass: 50751.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35014
#2: Chemical
ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE -23, INITIAL MET, RESIDUES -22 TO -17, HIS TAG, RESIDUES -16 TO 0, CLONING ARTIFACT, SAME ...RESIDUE -23, INITIAL MET, RESIDUES -22 TO -17, HIS TAG, RESIDUES -16 TO 0, CLONING ARTIFACT, SAME AS IN ENTRY 2BAS

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M SODIUM ACETATE THRIHYDRATE, 0.1M IMIDAZOLE, 0.1M TRIS HYDROCHLORIDE, 28% PEG 4000, 3% GLYCEROL, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→69.84 Å / Num. obs: 21459 / % possible obs: 87.2 % / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.83 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.66 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BAS

2bas


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 49.154 / SU ML: 0.423 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1046 4.9 %RANDOM
Rwork0.226 ---
obs0.228 20362 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.96 Å2
Baniso -1Baniso -2Baniso -3
1-7.38 Å20 Å20 Å2
2---8.51 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6634 0 94 7 6735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226799
X-RAY DIFFRACTIONr_bond_other_d0.0020.024619
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9819211
X-RAY DIFFRACTIONr_angle_other_deg0.833311180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39524.579356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.174151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5671536
X-RAY DIFFRACTIONr_chiral_restr0.0660.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027502
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021434
X-RAY DIFFRACTIONr_nbd_refined0.2220.21547
X-RAY DIFFRACTIONr_nbd_other0.190.24681
X-RAY DIFFRACTIONr_nbtor_refined0.1920.23341
X-RAY DIFFRACTIONr_nbtor_other0.0860.23739
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2143
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3030.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3060.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9051.54102
X-RAY DIFFRACTIONr_mcbond_other0.1481.51605
X-RAY DIFFRACTIONr_mcangle_it1.40126362
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28133179
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4314.52849
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2418tight positional0.030.05
21A1210tight positional0.030.05
31A584tight positional0.040.05
41A404tight positional0.030.05
42B404tight positional0.030.05
11A2418tight thermal0.080.5
21A1210tight thermal0.110.5
31A584tight thermal0.110.5
41A404tight thermal0.090.5
42B404tight thermal0.090.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 60 -
Rwork0.367 1103 -
obs--63.76 %
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)
12.2685-0.1844-1.44461.52121.7458.2056-0.2029-0.15590.18450.46910.02030.14320.8403-0.19790.1826-0.0234-0.01330.07480.4039-0.0365-0.350724.65959.30684.317
23.7641.3042-1.25123.32730.58714.3782-0.08710.2883-0.1579-0.3362-0.12530.17210.4185-0.08390.2124-0.5070.0492-0.00820.4066-0.0432-0.407827.71755.99438.684
30.89970.871-0.59977.306-0.13661.74630.1534-0.1380.38680.2118-0.06580.0956-0.46580.036-0.0877-0.4226-0.00250.02810.4533-0.0164-0.290336.79984.27154.062
41.66121.3526-0.53216.3863-0.28512.1197-0.1427-0.1169-0.31940.81530.0404-0.42851.54340.3140.10230.41540.1904-0.00250.54530.0325-0.274938.60939.14561.109
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 250
2X-RAY DIFFRACTION1A501 - 503
3X-RAY DIFFRACTION2A251 - 400
4X-RAY DIFFRACTION3B2 - 250
5X-RAY DIFFRACTION3B501 - 503
6X-RAY DIFFRACTION4B251 - 406

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