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- PDB-2vfk: AKAP18 delta central domain - AMP -

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Basic information

Entry
Database: PDB / ID: 2vfk
TitleAKAP18 delta central domain - AMP
ComponentsAKAP18 DELTA
KeywordsHYDROLASE / APO
Function / homologyCyclic Phosphodiesterase; Chain: A, / Cyclic phosphodiesterase / Alpha-Beta Complex / Alpha Beta / ADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsGold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Akap18 Contains a Phosphoesterase Domain that Binds AMP
Authors: Gold, M.G. / Smith, F.D. / Scott, J.D. / Barford, D.
History
DepositionNov 5, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

Downloads & links

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Assembly

Deposited unit
A: AKAP18 DELTA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5742
Polymers23,2271
Non-polymers3471
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.233, 42.233, 97.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein AKAP18 DELTA


Mass: 23226.936 Da / Num. of mol.: 1 / Fragment: RESIDUES 88-292
Source method: isolated from a genetically manipulated source
Details: 2H PHOSPHOESTERASE DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M TRIS HCL PH 8, 10 % PEG 8K, 7 MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.9794
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 30, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→97.59 Å / Num. obs: 31159 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO STRUCTURE

Resolution: 1.5→97.59 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.952 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1570 5 %RANDOM
Rwork0.161 ---
obs0.163 29583 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→97.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 23 217 1860
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9952265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8965206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4152572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00715315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.956156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021224
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.2776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21167
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2157
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4191.51043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01921640
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0833712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3784.5624
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 113
Rwork0.237 2150

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