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- PDB-4s1c: Crystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain -

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Basic information

Entry
Database: PDB / ID: 4s1c
TitleCrystal Structure of L. monocytogenes phosphodiesterase PgpH HD domain
ComponentsLmo1466 protein
KeywordsHYDROLASE / c-di-AMP / Listeria monocytogenes / phosphodiesterase / HD domain
Function / homology
Function and homology information


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
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_auth_seq_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

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Assembly

Deposited unit
D: Lmo1466 protein
A: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4696
Polymers50,2462
Non-polymers2234
Water3,351186
1
A: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2343
Polymers25,1231
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Lmo1466 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2343
Polymers25,1231
Non-polymers1122
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)50,4696
Polymers50,2462
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_564-x+y,-x+1,z-1/31
Buried area1990 Å2
ΔGint-70 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.562, 116.562, 91.783
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 / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 3.58 Å3/Da / Density % sol: 65.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350, pH 6.5, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.398→25 Å / Num. obs: 27548 / % possible obs: 98.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 33.61 Å2 / Rmerge(I) obs: 0.121 / Χ2: 1.01 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.493.80.40627251.29197.9
2.49-2.593.80.30427311.074198.4
2.59-2.73.80.24627291.019198
2.7-2.843.90.19427310.998198.7
2.84-3.023.90.15927471198.7
3.02-3.263.90.13627430.891198.7
3.26-3.583.90.11827450.957198.9
3.58-4.13.80.11327790.971199.2
4.1-5.163.80.09727810.982199.4
5.16-253.80.0928370.929199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→24.6 Å / SU ML: 0.3 / σ(F): 1.36 / Phase error: 25.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.231 1999 7.26 %
Rwork0.1847 --
obs0.1881 27525 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.95 Å2 / Biso mean: 39.7261 Å2 / Biso min: 18.16 Å2
Refinement stepCycle: LAST / Resolution: 2.398→24.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 4 186 3489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093365
X-RAY DIFFRACTIONf_angle_d1.1164551
X-RAY DIFFRACTIONf_chiral_restr0.042522
X-RAY DIFFRACTIONf_plane_restr0.007582
X-RAY DIFFRACTIONf_dihedral_angle_d13.891275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3976-2.45750.33681410.27991820196198
2.4575-2.52390.33461430.24471798194198
2.5239-2.59810.30971380.22161807194598
2.5981-2.68190.25671400.20821802194298
2.6819-2.77760.24361420.20141816195898
2.7776-2.88870.26841410.18891789193099
2.8887-3.01990.27071420.20181839198199
3.0199-3.17880.26091410.19811802194398
3.1788-3.37750.25471480.1981827197599
3.3775-3.63750.24881400.19741844198499
3.6375-4.00220.1891430.16461817196099
4.0022-4.57810.20561420.149818371979100
4.5781-5.75570.19231460.166918562002100
5.7557-24.60130.18071520.1641872202499

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