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- PDB-1soj: CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX -

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Basic information

Entry
Database: PDB / ID: 1soj
TitleCATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH IBMX
ComponentscGMP-inhibited 3',5'-cyclic phosphodiesterase B
KeywordsHYDROLASE / PDE3B PHOSPHODIESTERASE
Function / homology
Function and homology information


cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / PDE3B signalling / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / protein kinase B binding / negative regulation of cell adhesion mediated by integrin / guanyl-nucleotide exchange factor complex / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of cell adhesion / 3',5'-cyclic-nucleotide phosphodiesterase / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...cGMP-inhibited cyclic-nucleotide phosphodiesterase activity / PDE3B signalling / calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity / protein kinase B binding / negative regulation of cell adhesion mediated by integrin / guanyl-nucleotide exchange factor complex / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of cell adhesion / 3',5'-cyclic-nucleotide phosphodiesterase / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of angiogenesis / negative regulation of lipid catabolic process / negative regulation of angiogenesis / cAMP-mediated signaling / cellular response to insulin stimulus / G alpha (s) signalling events / angiogenesis / G protein-coupled receptor signaling pathway / Golgi apparatus / endoplasmic reticulum / membrane / metal ion binding / cytosol
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-ISOBUTYL-1-METHYLXANTHINE / cGMP-inhibited 3',5'-cyclic phosphodiesterase 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsScapin, G. / Patel, S.B. / Chung, C. / Varnerin, J.P. / Edmondson, S.D. / Mastracchio, A. / Parmee, E.R. / Becker, J.W. / Singh, S.B. / Van Der Ploeg, L.H. / Tota, M.R.
CitationJournal: Biochemistry / Year: 2004
Title: Crystal Structure of Human Phosphodiesterase 3B: Atomic Basis for Substrate and Inhibitor Specificity
Authors: Scapin, G. / Patel, S.B. / Chung, C. / Varnerin, J.P. / Edmondson, S.D. / Mastracchio, A. / Parmee, E.R. / Singh, S.B. / Becker, J.W. / Van Der Ploeg, L.H. / Tota, M.R.
History
DepositionMar 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
B: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
C: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
D: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
E: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
F: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
G: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
H: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
I: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
J: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
K: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
L: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)581,15648
Polymers577,90512
Non-polymers3,25036
Water5,188288
1
A: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
B: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
D: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
F: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
H: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
J: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
L: cGMP-inhibited 3',5'-cyclic phosphodiesterase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,8598
Polymers96,3182
Non-polymers5426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)275.046, 147.078, 253.485
Angle α, β, γ (deg.)90.00, 109.84, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
cGMP-inhibited 3',5'-cyclic phosphodiesterase B / Cyclic GMP inhibited phosphodiesterase B / CGI-PDE B / CGIPDE1 / CGIP1


Mass: 48158.781 Da / Num. of mol.: 12 / Fragment: catalytic domain, residues 654-1073
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE3B / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): CodonPlus
References: UniProt: Q13370, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Fragment: MG / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-IBM / 3-ISOBUTYL-1-METHYLXANTHINE


Mass: 222.244 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H14N4O2 / Comment: inhibitor, antagonist*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 4.81 Å3/Da / Density % sol: 74.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Peg MME, MES, MAgnesium Sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.9→50 Å / Num. all: 209980 / Num. obs: 203261 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 65.4 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 1.2 / Num. unique all: 17306 / % possible all: 82.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNXrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F0J

1f0j


Resolution: 2.9→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.249 10121 4.8 %RANDOM
Rwork0.231 ---
obs0.235 203114 97.7 %-
all-209937 --
Solvent computationSolvent model: MASK / Bsol: 20.8 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.88 Å20 Å2-5.03 Å2
2---20.683 Å20 Å2
3---10.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35544 0 216 288 36048
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d20.33
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.452
X-RAY DIFFRACTIONc_scbond_it2.442
X-RAY DIFFRACTIONc_scangle_it3.92.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)Weight Biso Weight position
11RESTRAINEDX-RAY DIFFRACTION0.0222300
22X-RAY DIFFRACTION0.0232300
LS refinement shellResolution: 2.9→3 Å
RfactorNum. reflection% reflection
Rfree0.401 889 4.3 %
Rwork0.383 17179 -
obs-17179 82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM

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