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- PDB-5xsp: The catalytic domain of GdpP with 5'-pApA -

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Basic information

Entry
Database: PDB / ID: 5xsp
TitleThe catalytic domain of GdpP with 5'-pApA
Components
  • DNA (5'-R(P*AP*A)-3')
  • Phosphodiesterase 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 / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Cyclic-di-AMP phosphodiesterase GdpP/PdeA / : / Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain / Cyclic-di-AMP phosphodiesterase GdpP-like, GGDEF domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain ...Cyclic-di-AMP phosphodiesterase GdpP/PdeA / : / Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain / Cyclic-di-AMP phosphodiesterase GdpP-like, GGDEF domain / : / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain
Similarity search - Domain/homology
: / RNA / Cyclic-di-AMP phosphodiesterase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.146 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 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_type.id
Revision 2.0May 29, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_comp_id
Revision 3.0Apr 30, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _chem_comp_bond.pdbx_aromatic_flag / _chem_comp_bond.value_order / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_gene_src_gene / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_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_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphodiesterase acting on cyclic dinucleotides
B: Phosphodiesterase acting on cyclic dinucleotides
C: DNA (5'-R(P*AP*A)-3')
D: DNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7098
Polymers77,4894
Non-polymers2204
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-28 kcal/mol
Surface area28040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.619, 117.263, 127.368
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0U1MUE2
#2: RNA chain DNA (5'-R(P*AP*A)-3')


Mass: 613.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% (w/v) PEG8000, 0.1 M imidazole pH 7.5, 0.2 M 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: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 45475 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 38.4
Reflection shellResolution: 2.15→38.1 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.491 / % possible all: 82

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XSI

5xsi


Resolution: 2.146→38.132 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 2177 5 %
Rwork0.1966 --
obs0.1989 43529 95.43 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.523 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5591 Å2-0 Å20 Å2
2---5.6854 Å20 Å2
3---2.1263 Å2
Refinement stepCycle: LAST / Resolution: 2.146→38.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5171 0 94 316 5581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085339
X-RAY DIFFRACTIONf_angle_d1.017256
X-RAY DIFFRACTIONf_dihedral_angle_d13.0212000
X-RAY DIFFRACTIONf_chiral_restr0.064873
X-RAY DIFFRACTIONf_plane_restr0.006924
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1457-2.19240.30171140.23872206X-RAY DIFFRACTION82
2.1924-2.24340.29081300.22682404X-RAY DIFFRACTION91
2.2434-2.29950.29591140.24622515X-RAY DIFFRACTION93
2.2995-2.36160.27261250.23362391X-RAY DIFFRACTION89
2.3616-2.43110.27531320.21912499X-RAY DIFFRACTION94
2.4311-2.50960.32011330.2192550X-RAY DIFFRACTION95
2.5096-2.59920.25771430.21482585X-RAY DIFFRACTION96
2.5992-2.70330.28751440.22112569X-RAY DIFFRACTION97
2.7033-2.82630.3031350.22272599X-RAY DIFFRACTION97
2.8263-2.97520.27861350.21922654X-RAY DIFFRACTION98
2.9752-3.16160.26041490.21342645X-RAY DIFFRACTION98
3.1616-3.40550.2281420.2112687X-RAY DIFFRACTION99
3.4055-3.7480.24661310.19222684X-RAY DIFFRACTION99
3.748-4.28970.19461480.15982731X-RAY DIFFRACTION99
4.2897-5.40210.1921600.15682757X-RAY DIFFRACTION100
5.4021-38.13770.23211420.18672876X-RAY DIFFRACTION99

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