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- PDB-5xsi: The catalytic domain of GdpP -

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Basic information

Entry
Database: PDB / ID: 5xsi
TitleThe catalytic domain of GdpP
ComponentsPhosphodiesterase acting on cyclic dinucleotides
KeywordsHYDROLASE / phosphodiesterase
Function / homology
Function and homology information


cyclic-di-AMP phosphodiesterase activity / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / nucleic acid binding / hydrolase activity / metal ion binding / plasma membrane
Similarity search - Function
: / Cyclic-di-AMP phosphodiesterase GdpP, PAS domain / Cyclic-di-AMP phosphodiesterase GdpP/PdeA / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain
Similarity search - Domain/homology
: / Cyclic-di-AMP phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsWang, F. / Gu, L.
CitationJournal: Biochem. J. / Year: 2018
Title: Structural and biochemical characterization of the catalytic domains of GdpP reveals a unified hydrolysis mechanism for the DHH/DHHA1 phosphodiesterase
Authors: Wang, F. / He, Q. / Su, K. / Wei, T. / Xu, S. / Gu, L.
History
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphodiesterase acting on cyclic dinucleotides
B: Phosphodiesterase acting on cyclic dinucleotides
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4826
Polymers76,2622
Non-polymers2204
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-39 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.085, 117.091, 127.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphodiesterase acting on cyclic dinucleotides


Mass: 38131.156 Da / Num. of mol.: 2 / Fragment: UNP residues 322-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: cdnD, BN1321_430104 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U1MUE2
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10%(w/v) PEG8000, 0.1M imidazole pH 7.5, 0.2M calcium acetate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 43266 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.09 / Net I/σ(I): 23.61
Reflection shellResolution: 2.2→46.4 Å / Redundancy: 6.5 % / Rsym value: 0.433 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.421 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.69
RfactorNum. reflection% reflection
Rfree0.2258 2170 5.02 %
Rwork0.1736 --
obs0.1763 43195 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 4 340 5538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195262
X-RAY DIFFRACTIONf_angle_d1.527132
X-RAY DIFFRACTIONf_dihedral_angle_d15.4083228
X-RAY DIFFRACTIONf_chiral_restr0.09856
X-RAY DIFFRACTIONf_plane_restr0.01924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1877-2.23860.26471230.19742552X-RAY DIFFRACTION95
2.2386-2.29450.26171530.19962728X-RAY DIFFRACTION100
2.2945-2.35660.25271430.20042703X-RAY DIFFRACTION100
2.3566-2.42590.27641540.20412686X-RAY DIFFRACTION100
2.4259-2.50420.25261150.20392760X-RAY DIFFRACTION100
2.5042-2.59370.28421470.1962710X-RAY DIFFRACTION100
2.5937-2.69750.29751280.18742720X-RAY DIFFRACTION100
2.6975-2.82030.251540.19252709X-RAY DIFFRACTION100
2.8203-2.9690.25251380.18632737X-RAY DIFFRACTION100
2.969-3.15490.27971400.19472753X-RAY DIFFRACTION100
3.1549-3.39850.19541500.19052731X-RAY DIFFRACTION100
3.3985-3.74030.2261380.17212778X-RAY DIFFRACTION100
3.7403-4.28120.20281760.14722736X-RAY DIFFRACTION100
4.2812-5.39260.17261580.13862805X-RAY DIFFRACTION100
5.3926-46.4310.21641530.16462917X-RAY DIFFRACTION99

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