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- PDB-1woj: Crystal structure of human phosphodiesterase -

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Basic information

Entry
Database: PDB / ID: 1woj
TitleCrystal structure of human phosphodiesterase
Components2',3'-cyclic-nucleotide 3'-phosphodiesterase
KeywordsHYDROLASE
Function / homology
Function and homology information


cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / : / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium ...cyclic nucleotide catabolic process / 2',3'-cyclic-nucleotide 3'-phosphodiesterase / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / : / myelin sheath adaxonal region / myelin sheath abaxonal region / cyclic nucleotide binding / regulation of mitochondrial membrane permeability / oligodendrocyte differentiation / pseudopodium / microvillus / forebrain development / substantia nigra development / axonogenesis / adult locomotory behavior / response to toxic substance / microtubule cytoskeleton organization / melanosome / chemical synaptic transmission / mitochondrial inner membrane / microtubule / mitochondrial outer membrane / response to lipopolysaccharide / synapse / perinuclear region of cytoplasm / extracellular space / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
2',3'-cyclic nucleotide 3'-phosphodiesterase fold / 2',3'-cyclic nucleotide 3'-phosphodiesterase superfamily / Cyclic nucleotide phosphodiesterase / 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase) / Cyclic phosphodiesterase / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.8 Å
AuthorsSakamoto, Y. / Tanaka, N. / Ichimiya, T. / Kurihara, T. / Nakamura, K.T.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of the catalytic fragment of human brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase
Authors: Sakamoto, Y. / Tanaka, N. / Ichimiya, T. / Kurihara, T. / Nakamura, K.T.
History
DepositionAug 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2',3'-cyclic-nucleotide 3'-phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0412
Polymers23,9461
Non-polymers951
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.386, 55.348, 78.757
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 2',3'-cyclic-nucleotide 3'-phosphodiesterase / / CNP / CNPase


Mass: 23946.387 Da / Num. of mol.: 1 / Fragment: residues 166-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P09543, 2',3'-cyclic-nucleotide 3'-phosphodiesterase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 1.91 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG300, sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 18263 / % possible obs: 98.2 % / Redundancy: 6.5 % / Rsym value: 0.057 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.191 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SIR / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.435 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 934 5.1 %RANDOM
Rwork0.19238 ---
obs0.19406 17284 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1646 0 5 96 1747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211684
X-RAY DIFFRACTIONr_bond_other_d0.0020.021540
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9772269
X-RAY DIFFRACTIONr_angle_other_deg0.72133595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3665207
X-RAY DIFFRACTIONr_chiral_restr0.0630.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02345
X-RAY DIFFRACTIONr_nbd_refined0.2050.2271
X-RAY DIFFRACTIONr_nbd_other0.2340.21664
X-RAY DIFFRACTIONr_nbtor_other0.0790.21016
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1070.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0960.211
X-RAY DIFFRACTIONr_mcbond_it0.7091.51032
X-RAY DIFFRACTIONr_mcangle_it1.37921650
X-RAY DIFFRACTIONr_scbond_it2.1533652
X-RAY DIFFRACTIONr_scangle_it3.7324.5619
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 65
Rwork0.209 1132

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