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- PDB-4lyk: Crystal structure of the EAL domain of c-di-GMP specific phosphod... -

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Basic information

Entry
Database: PDB / ID: 4lyk
TitleCrystal structure of the EAL domain of c-di-GMP specific phosphodiesterase YahA in complex with activating cofactor Mg++
ComponentsCyclic di-GMP phosphodiesterase YahA
KeywordsHYDROLASE / pGpG / phosphodiesterase / TIM-barrel
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / transcription cis-regulatory region binding / positive regulation of DNA-templated transcription / protein homodimerization activity / metal ion binding / plasma membrane
Similarity search - Function
EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family ...EAL domain / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
trans-4-(hydroxymethyl)cyclohexanol / Cyclic di-GMP phosphodiesterase PdeL
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSundriyal, A. / Schirmer, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Inherent Regulation of EAL Domain-catalyzed Hydrolysis of Second Messenger Cyclic di-GMP.
Authors: Sundriyal, A. / Massa, C. / Samoray, D. / Zehender, F. / Sharpe, T. / Jenal, U. / Schirmer, T.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclic di-GMP phosphodiesterase YahA
B: Cyclic di-GMP phosphodiesterase YahA
C: Cyclic di-GMP phosphodiesterase YahA
D: Cyclic di-GMP phosphodiesterase YahA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,25117
Polymers124,3234
Non-polymers92813
Water4,197233
1
A: Cyclic di-GMP phosphodiesterase YahA
B: Cyclic di-GMP phosphodiesterase YahA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6579
Polymers62,1612
Non-polymers4957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-21 kcal/mol
Surface area21470 Å2
MethodPISA
2
C: Cyclic di-GMP phosphodiesterase YahA
D: Cyclic di-GMP phosphodiesterase YahA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5948
Polymers62,1612
Non-polymers4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-25 kcal/mol
Surface area21230 Å2
MethodPISA
3
A: Cyclic di-GMP phosphodiesterase YahA
B: Cyclic di-GMP phosphodiesterase YahA
hetero molecules

C: Cyclic di-GMP phosphodiesterase YahA
D: Cyclic di-GMP phosphodiesterase YahA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,25117
Polymers124,3234
Non-polymers92813
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area8210 Å2
ΔGint-60 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.850, 109.547, 81.750
Angle α, β, γ (deg.)90.000, 99.390, 90.000
Int Tables number4
Space group name H-MP1211
Detailstwo biological units in the asym.

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Components

#1: Protein
Cyclic di-GMP phosphodiesterase YahA


Mass: 31080.678 Da / Num. of mol.: 4 / Fragment: EAL domain containing residues 101-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0315, JW0307, yahA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21514, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-HB0 / trans-4-(hydroxymethyl)cyclohexanol


Mass: 130.185 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H14O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 10 % of amino acid mixture (200 mM of each of Sodium-L-glutamate, M DL-alanine, Glycin and L-Lysine HCl, 0.2 M DL-Serin), 100 mM ...Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 10 % of amino acid mixture (200 mM of each of Sodium-L-glutamate, M DL-alanine, Glycin and L-Lysine HCl, 0.2 M DL-Serin), 100 mM MES/Imidazole pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→109.55 Å / Num. obs: 43912 / % possible obs: 99.63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.5822
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
2.4-2.533.310.451.7621003634499.79
2.53-2.683.60.322.4521877608099.93
2.68-2.873.560.223.6620257568499.76
2.87-3.13.490.135.9418628533499.84
3.1-3.393.280.0810.4616028488499.75
3.39-3.793.220.0417.9214213441299.58
3.79-4.383.490.0325.1813609390499.58
4.38-5.373.360.0328.7411053329199.21
5.37-7.593.080.0327.767830254298.56
7.59-109.553.450.0234.484961143799

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
SCALACCP4_3.3.20data scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIE

4kie


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0 / SU B: 15.811 / SU ML: 0.18 / σ(F): 0 / ESU R: 0.442 / ESU R Free: 0.241 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.222 2209 5 %
Rwork0.1886 --
obs0.1902 43884 99.58 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.6 Å2 / Biso mean: 50.282 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å2-0 Å2-1.56 Å2
2---0.18 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7881 0 60 233 8174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228164
X-RAY DIFFRACTIONr_bond_other_d0.0070.027910
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.96611087
X-RAY DIFFRACTIONr_angle_other_deg1.1923.00218247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40351011
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80725.144348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.533151338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8171524
X-RAY DIFFRACTIONr_chiral_restr0.0810.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219121
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021765
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 152 -
Rwork0.29 3015 -
all-3167 -
obs--99.69 %
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)
12.3026-0.3886-1.44631.31270.22142.6862-0.0595-0.3240.07220.14120.1740.07130.02810.4429-0.11450.2918-0.00330.10550.2519-0.01760.0454-0.6276.7258.768
21.8927-0.54960.29011.6437-0.43422.24520.15380.14850.1952-0.2596-0.05750.0001-0.03990.06-0.09640.3226-0.00560.12940.2329-0.01790.07981.6249.152-27.784
31.6560.09881.61231.84230.15592.53270.00090.62590.0585-0.0905-0.1012-0.2895-0.12340.74540.10030.2278-0.04550.12940.37310.02990.122731.165-14.661-4.544
43.0840.6217-0.05052.1629-0.26181.5411-0.0504-0.1792-0.08060.2655-0.0123-0.16940.0060.01260.06270.2602-0.0576-0.02810.1514-0.02420.088336.725-21.55131.228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A107 - 359
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B107 - 359
4X-RAY DIFFRACTION2B401 - 402
5X-RAY DIFFRACTION3C107 - 358
6X-RAY DIFFRACTION3C401 - 402
7X-RAY DIFFRACTION4D106 - 358
8X-RAY DIFFRACTION4D401 - 402

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