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- PDB-5o7f: Structure of the inactive T.maritima PDE (TM1595) D80N D154N muta... -

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Basic information

Entry
Database: PDB / ID: 5o7f
TitleStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with GMP and Mn2+
Componentsphosphodiesterase
KeywordsHYDROLASE / phosphodiesterase
Function / homology
Function and homology information


nucleic acid binding / nucleotide binding / metal ion binding
Similarity search - Function
: / DDH domain / DHH family / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / : / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsWitte, G. / Drexler, D. / Mueller, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation3717/3-1 Germany
German Research FoundationGRK1721 Germany
CitationJournal: Structure / Year: 2017
Title: Structural and Biophysical Analysis of the Soluble DHH/DHHA1-Type Phosphodiesterase TM1595 from Thermotoga maritima.
Authors: Drexler, D.J. / Muller, M. / Rojas-Cordova, C.A. / Bandera, A.M. / Witte, G.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: phosphodiesterase
B: phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,05614
Polymers75,7382
Non-polymers1,31912
Water9,926551
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Molecular weight is confirmed by static light scattering (dimer), SAXS, SAXS curve is only compatible with the biological dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-32 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.900, 105.620, 134.460
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


Mass: 37868.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: TM_1595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1T1
#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% w/v PEG4000, 0.1M TRIS pH 8.5, 0.2M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.2999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2999 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 120906 / % possible obs: 99.7 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rrim(I) all: 0.072 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.89 / Num. unique obs: 8954 / CC1/2: 0.75 / Rrim(I) all: 1.305 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→46.375 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2055 1967 3.15 %
Rwork0.1649 --
obs0.1662 62477 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→46.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5107 0 76 551 5734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085334
X-RAY DIFFRACTIONf_angle_d0.8637220
X-RAY DIFFRACTIONf_dihedral_angle_d2.64371
X-RAY DIFFRACTIONf_chiral_restr0.062795
X-RAY DIFFRACTIONf_plane_restr0.005929
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8999-1.94750.31581310.25824083X-RAY DIFFRACTION94
1.9475-2.00010.24131330.2294154X-RAY DIFFRACTION96
2.0001-2.0590.2431360.20344170X-RAY DIFFRACTION96
2.059-2.12540.23241370.18694210X-RAY DIFFRACTION97
2.1254-2.20140.20951380.17034218X-RAY DIFFRACTION97
2.2014-2.28950.20651390.16194292X-RAY DIFFRACTION99
2.2895-2.39370.22041420.15784350X-RAY DIFFRACTION99
2.3937-2.51990.19291410.16024349X-RAY DIFFRACTION99
2.5199-2.67780.21961420.16164329X-RAY DIFFRACTION99
2.6778-2.88450.18951440.16324377X-RAY DIFFRACTION100
2.8845-3.17470.20941410.16294393X-RAY DIFFRACTION99
3.1747-3.6340.20581450.14884439X-RAY DIFFRACTION100
3.634-4.57780.1711460.14074473X-RAY DIFFRACTION100
4.5778-46.38910.2121520.17714673X-RAY DIFFRACTION100
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)
12.5614-0.303-0.05262.18660.55711.60480.0133-0.21360.37530.3457-0.11060.2515-0.3249-0.2036-0.00120.31210.01470.03930.2941-0.050.295722.49378.840783.0642
21.60630.0364-0.14251.14760.32861.1741-0.0319-0.12420.10930.14170.1275-0.0337-0.16510.1381-0.02740.2807-0.0253-0.00270.2859-0.01810.26530.301677.685776.7367
30.87580.4263-0.19011.90541.0932.46110.0134-0.32770.26270.11120.383-0.3264-0.13010.7936-0.12040.3078-0.0361-0.00210.3465-0.0920.348436.603877.273876.0014
41.58720.1-0.39321.3011-0.26050.85470.0916-0.4842-0.04750.3936-0.0783-0.05430.00960.0512-0.02670.3795-0.00540.010.3577-0.01120.277125.684771.902388.8226
51.31830.0903-0.35931.24020.79531.71160.02450.05670.0172-0.0491-0.03390.1089-0.0902-0.05710.00550.2320.0093-0.00970.26550.00180.247118.796670.424170.0437
61.841-0.0428-0.1311.06210.24751.75470.1135-0.1052-0.35130.032-0.1602-0.23960.36060.5038-0.04540.30040.0249-0.02030.4031-0.00880.327938.073851.986670.5516
71.38930.1685-0.4760.98620.03921.27480.0862-0.3697-0.14690.2277-0.1422-0.12290.24680.2642-0.06590.3470.0177-0.04450.45680.07230.315735.71251.390176.2805
81.2135-0.074-0.04981.78490.65852.2119-0.0533-0.4567-0.32290.25490.05660.020.0916-0.0633-0.02940.3764-0.02280.00310.40930.06550.300525.626551.716984.4587
94.13770.4524-0.37132.30090.26642.46520.2037-1.0881-0.30780.7873-0.2491-0.16310.66040.0308-0.05940.5444-0.0262-0.01050.50760.21470.39127.689842.263287.6622
101.98320.14310.30961.15150.15721.84430.03880.3411-0.1637-0.0734-0.05170.0555-0.0661-0.01420.04180.2417-0.0091-0.0040.2677-0.05310.25579.134249.528941.6673
111.6309-0.01590.64291.08490.43362.3563-0.03010.1565-0.1358-0.0926-0.00820.02330.03070.06830.02040.1884-0.01810.00020.2178-0.01210.228314.110353.506144.8955
122.6433-0.2304-0.82320.53790.31431.5805-0.04750.115-0.2894-0.07520.0572-0.09530.13170.1201-0.04890.26930.0032-0.01120.2415-0.05570.26835.66348.943950.975
132.5244-0.1471-0.07624.59430.76272.62170.12040.40320.0242-0.50910.0183-0.4534-0.36690.1663-0.09970.3018-0.00420.03050.4391-0.04860.320245.49155.523439.5511
140.55760.2065-0.05580.08650.27381.03370.18470.1925-0.11330.06590.3206-0.11080.23020.1722-0.07040.50180.0366-0.02620.7271-0.01630.594428.702155.107962.279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 74 )
4X-RAY DIFFRACTION4chain 'A' and (resid 75 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 176 )
6X-RAY DIFFRACTION6chain 'A' and (resid 177 through 227 )
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 268 )
8X-RAY DIFFRACTION8chain 'A' and (resid 269 through 298 )
9X-RAY DIFFRACTION9chain 'A' and (resid 299 through 319 )
10X-RAY DIFFRACTION10chain 'B' and (resid -1 through 53 )
11X-RAY DIFFRACTION11chain 'B' and (resid 54 through 176 )
12X-RAY DIFFRACTION12chain 'B' and (resid 177 through 298 )
13X-RAY DIFFRACTION13chain 'B' and (resid 299 through 318 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 2 )

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