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- PDB-1jh7: Semi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase ... -

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Basic information

Entry
Database: PDB / ID: 1jh7
TitleSemi-reduced Inhibitor-bound Cyclic Nucleotide Phosphodiesterase from Arabidopsis thaliana
Componentscyclic phosphodiesterase
KeywordsHYDROLASE / ADP-ribose 1'' / 2''-cyclic phosphate / RNA processing / 2' / 3'-cyclic nucleotide phosphodiesterase / 3'-cyclic uridine vanadate
Function / homology
Function and homology information


cyclic-nucleotide phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / tRNA splicing, via endonucleolytic cleavage and ligation / cytoplasm / cytosol
Similarity search - Function
2',3'-cyclic-nucleotide 3'-phosphodiesterase / Cyclic phosphodiesterase-like protein / Cyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
URIDINE-2',3'-VANADATE / Cyclic phosphodiesterase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structures of the semireduced and inhibitor-bound forms of cyclic nucleotide phosphodiesterase from Arabidopsis thaliana.
Authors: Hofmann, A. / Grella, M. / Botos, I. / Filipowicz, W. / Wlodawer, A.
History
DepositionJun 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5817
Polymers21,5101
Non-polymers1,0716
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: cyclic phosphodiesterase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)135,48542
Polymers129,0626
Non-polymers6,42336
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area24670 Å2
ΔGint-385 kcal/mol
Surface area46230 Å2
MethodPISA
3
A: cyclic phosphodiesterase
hetero molecules

A: cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,16214
Polymers43,0212
Non-polymers2,14112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
MethodPQS
Unit cell
Length a, b, c (Å)101.140, 101.140, 90.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-213-

SO4

21A-214-

SO4

31A-214-

SO4

41A-215-

SO4

51A-215-

SO4

61A-377-

HOH

71A-392-

HOH

81A-393-

HOH

91A-394-

HOH

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Components

#1: Protein cyclic phosphodiesterase


Mass: 21510.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET11d+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O04147, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O9V
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.1 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5
Details: (NH4)2SO4, NaOAc, DTT, 2',3'-cyclic uridine vanadate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.2-2.0 Mammonium sulfate1reservoir
20.1 M1reservoirpH5.0NaOAc
312.5 mMDTT1drop
4100 mM1dropNaCl
520 mMTris-HCl1droppH8.0
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 7212 / Num. obs: 7212 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 38.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.466 / % possible all: 95.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 5960 / Num. measured all: 87738
Reflection shell
*PLUS
% possible obs: 95.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: semi-reduced CPDase (A. thaliana) [delta 90-115]

Resolution: 2.4→25.29 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 185038.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.399 650 10.9 %RANDOM
Rwork0.214 ---
obs-5960 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 236.9 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å26.95 Å20 Å2
2--0.85 Å20 Å2
3----1.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.4→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1458 0 62 94 1614
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.653
X-RAY DIFFRACTIONc_mcangle_it4.243.5
X-RAY DIFFRACTIONc_scbond_it4.093.5
X-RAY DIFFRACTIONc_scangle_it6.014
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.477 97 10.5 %
Rwork0.431 829 -
obs--79.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5UVD_NEU2.PARAMUVD_NEU2.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 10.9 % / Rfactor obs: 0.213 / Rfactor Rfree: 0.398
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.02
X-RAY DIFFRACTIONc_mcbond_it2.653
X-RAY DIFFRACTIONc_scbond_it4.093.5
X-RAY DIFFRACTIONc_mcangle_it4.243.5
X-RAY DIFFRACTIONc_scangle_it6.014
LS refinement shell
*PLUS
Rfactor Rfree: 0.477 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.431

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