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- PDB-4s1b: Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD d... -

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Basic information

Entry
Database: PDB / ID: 4s1b
TitleCrystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain in complex with Cyclic-di-AMP
ComponentsLmo1466 protein
KeywordsHYDROLASE / c-di-AMP / Listeria monocytogenes / phosphodiesterase / HD domain
Function / homology
Function and homology information


metal ion binding / membrane
Similarity search - Function
Metal-dependent phosphohydrolase, 7TM intracellular domain / Metal-dependent phosphohydrolase, 7TM extracellular domain / : / 7TM-HD extracellular / 7TM receptor with intracellular HD hydrolase / HDIG domain / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
Chem-2BA / : / Lmo1466 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.099 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: An HD-domain phosphodiesterase mediates cooperative hydrolysis of c-di-AMP to affect bacterial growth and virulence.
Authors: Huynh, T.N. / Luo, S. / Pensinger, D. / Sauer, J.D. / Tong, L. / Woodward, J.J.
History
DepositionJan 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_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: Lmo1466 protein
D: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7868
Polymers50,2462
Non-polymers1,5406
Water3,873215
1
A: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8934
Polymers25,1231
Non-polymers7703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8934
Polymers25,1231
Non-polymers7703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lmo1466 protein
hetero molecules

D: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7868
Polymers50,2462
Non-polymers1,5406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x-y,x,z+1/61
Buried area2610 Å2
ΔGint-18 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.286, 124.286, 58.019
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Lmo1466 protein


Mass: 25122.803 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo1466, pgpH / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y746
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M MgCl2, 0.1 M MES, 30% PEG 3350, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: single-wavelenth anomalous diffraction / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.099→25 Å / Num. obs: 29910 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 27.74 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.061 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.70.40829750.908199.7
2.18-2.2640.3429791.029199.8
2.26-2.3640.25929781.016199.8
2.36-2.493.80.22529741.074199.6
2.49-2.654.10.18629871.106199.8
2.65-2.8540.13929751.07199.9
2.85-3.144.30.11630111.0971100
3.14-3.594.10.09229891.078199.1
3.59-4.524.10.07529801.105198.6
4.52-254.20.07130621.103198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.099→24.693 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2024 1713 5.73 %
Rwork0.1625 --
obs0.1648 29902 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.05 Å2 / Biso mean: 29.8999 Å2 / Biso min: 14.48 Å2
Refinement stepCycle: LAST / Resolution: 2.099→24.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 92 215 3697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013560
X-RAY DIFFRACTIONf_angle_d1.2114842
X-RAY DIFFRACTIONf_chiral_restr0.055552
X-RAY DIFFRACTIONf_plane_restr0.006607
X-RAY DIFFRACTIONf_dihedral_angle_d15.5411360
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0986-2.16030.26981420.19372290243299
2.1603-2.230.24521440.187523442488100
2.23-2.30970.25231460.184423492495100
2.3097-2.40210.24781420.17623432485100
2.4021-2.51130.23161430.18372329247299
2.5113-2.64350.23021410.17123602501100
2.6435-2.80890.21991400.177923492489100
2.8089-3.02550.22341450.174823562501100
3.0255-3.32930.2171450.170623612506100
3.3293-3.80950.17361430.15012343248699
3.8095-4.79380.16651420.13222339248198
4.7938-24.69480.16921400.15592426256699

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