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- PDB-2xss: Crystal structure of GAFb from the human phosphodiesterase 5 -

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Basic information

Entry
Database: PDB / ID: 2xss
TitleCrystal structure of GAFb from the human phosphodiesterase 5
ComponentsCGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE
KeywordsHYDROLASE
Function / homology
Function and homology information


positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects ...positive regulation of oocyte development / 3',5'-cyclic-GMP phosphodiesterase / regulation of nitric oxide mediated signal transduction / negative regulation of cardiac muscle contraction / oocyte development / RHOBTB1 GTPase cycle / relaxation of cardiac muscle / cGMP catabolic process / positive regulation of cardiac muscle hypertrophy / cGMP effects / 3',5'-cyclic-nucleotide phosphodiesterase activity / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / Smooth Muscle Contraction / 3',5'-cyclic-AMP phosphodiesterase activity / negative regulation of T cell proliferation / T cell proliferation / cAMP-mediated signaling / metal ion binding / cytosol
Similarity search - Function
GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / 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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. ...GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / 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. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
cGMP-specific 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSchlicker, C. / Russwurm, M. / Steegborn, C.
CitationJournal: Proteins / Year: 2011
Title: Crystal Structure of the Gaf-B Domain from Human Phosphodiesterase 5.
Authors: Russwurm, M. / Schlicker, C. / Weyand, M. / Koesling, D. / Steegborn, C.
History
DepositionSep 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE
B: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE


Theoretical massNumber of molelcules
Total (without water)41,3472
Polymers41,3472
Non-polymers00
Water00
1
A: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE
B: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE

A: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE
B: CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE


Theoretical massNumber of molelcules
Total (without water)82,6944
Polymers82,6944
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area15850 Å2
ΔGint-135.3 kcal/mol
Surface area29940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.750, 64.750, 145.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CGMP-SPECIFIC 3', 5'-CYCLIC PHOSPHODIESTERASE / CGMP-BINDING CGMP-SPECIFIC PHOSPHODIESTERASE / CGB-PDE


Mass: 20673.607 Da / Num. of mol.: 2 / Fragment: GAFB DOMAIN, RESIDUES 346-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: O76074, 3',5'-cyclic-GMP phosphodiesterase
Sequence detailsGAFB DOMAIN COMPRISES RESIDUES 346 TO 503

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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: 2.13 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 16% PEG 3350, 0.06 M CITRIC ACID, 0.04 M BIS-TRIS PROPANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97881
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97881 Å / Relative weight: 1
ReflectionResolution: 2.5→44.39 Å / Num. obs: 12657 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.5→44.39 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / SU B: 38.354 / SU ML: 0.365 / Cross valid method: THROUGHOUT / ESU R: 0.614 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.31709 632 5 %RANDOM
Rwork0.24846 ---
obs0.25187 12023 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.642 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20.93 Å20 Å2
2--1.85 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 0 0 2377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222407
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9643227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5035298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32225.769104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.56215459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.543158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.51521
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18922449
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7043886
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6734.5778
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 45 -
Rwork0.333 853 -
obs--100 %
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)
12.10850.25690.34582.0591-0.59479.89860.12130.53080.64730.15210.09530.1854-0.73040.2893-0.21660.18750.08840.10130.22260.11420.325614.6978-16.961217.2446
21.9858-0.3608-0.03072.65830.86777.0870.50420.6637-0.64750.32610.1138-0.55161.30771.0365-0.6180.59690.4542-0.40380.4682-0.3060.479625.5329-43.553415.8834
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A339 - 508
2X-RAY DIFFRACTION2B343 - 509

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