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- PDB-5o4z: Structure of the inactive T.maritima PDE (TM1595) D80N D154N muta... -

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Basic information

Entry
Database: PDB / ID: 5o4z
TitleStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApA
ComponentsDHH/DHHA1-type phosphodiesterase TM1595
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
ADENOSINE-5'-MONOPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionMay 31, 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 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Data collection / Source and taxonomy / Category: pdbx_entity_src_syn
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DHH/DHHA1-type phosphodiesterase TM1595
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,39513
Polymers37,8691
Non-polymers1,52612
Water4,486249
1
A: DHH/DHHA1-type phosphodiesterase TM1595
hetero molecules

A: DHH/DHHA1-type phosphodiesterase TM1595
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,79026
Polymers75,7382
Non-polymers3,05224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)71.670, 87.830, 122.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

21A-635-

HOH

31A-672-

HOH

41A-698-

HOH

51A-740-

HOH

61A-742-

HOH

71A-749-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DHH/DHHA1-type phosphodiesterase TM1595


Mass: 37868.945 Da / Num. of mol.: 1 / Mutation: D80N D154N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_1595 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1T1

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Non-polymers , 5 types, 261 molecules

#2: Chemical ChemComp-A / ADENOSINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.2M Ammoniumsulfate 0.1 M Sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 42319 / % possible obs: 98.8 % / Redundancy: 9.9 % / CC1/2: 0.99 / Net I/σ(I): 21.4
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.25 / Num. unique obs: 3050 / CC1/2: 0.766 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O1U

5o1u


Resolution: 1.7→43.915 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.04
RfactorNum. reflection% reflection
Rfree0.1962 2014 4.76 %
Rwork0.1731 --
obs0.1741 42286 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2568 45 44 249 2906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062748
X-RAY DIFFRACTIONf_angle_d0.7633733
X-RAY DIFFRACTIONf_dihedral_angle_d11.661622
X-RAY DIFFRACTIONf_chiral_restr0.055405
X-RAY DIFFRACTIONf_plane_restr0.005473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.38751470.37142785X-RAY DIFFRACTION98
1.7425-1.78960.34141290.30962891X-RAY DIFFRACTION99
1.7896-1.84230.30031520.26322837X-RAY DIFFRACTION99
1.8423-1.90170.31961430.2732732X-RAY DIFFRACTION95
1.9017-1.96970.33011160.28362758X-RAY DIFFRACTION95
1.9697-2.04860.21561520.20082859X-RAY DIFFRACTION99
2.0486-2.14180.21091550.20612847X-RAY DIFFRACTION99
2.1418-2.25470.23241480.19112877X-RAY DIFFRACTION99
2.2547-2.3960.19041340.17092886X-RAY DIFFRACTION99
2.396-2.58090.19151770.16882894X-RAY DIFFRACTION100
2.5809-2.84060.20521450.16892910X-RAY DIFFRACTION100
2.8406-3.25160.19251290.1652943X-RAY DIFFRACTION100
3.2516-4.09610.15631350.14322979X-RAY DIFFRACTION100
4.0961-43.92960.16771520.15133074X-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)
10.86280.7825-0.06481.89850.10990.94960.1237-0.1410.0020.2119-0.10040.0152-0.0483-0.0636-0.02690.2467-0.01260.00140.274-0.0160.2264-3.5698-9.7724-14.4268
20.36770.1003-0.3110.93970.36321.70810.2090.0549-0.11010.0370.09860.03830.11020.0243-0.19890.559-0.1133-0.05730.4875-0.01420.47722.2838-8.2628-14.1779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -2 through 320)
2X-RAY DIFFRACTION2(chain 'E' and resid 1 through 2)

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