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- PDB-5xby: Crystal structure of the PKA-Protein A fusion protein (end-to-end... -

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Basic information

Entry
Database: PDB / ID: 5xby
TitleCrystal structure of the PKA-Protein A fusion protein (end-to-end fusion)
ComponentscAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / synthetic protein / kinase / LYASE
Function / homology
Function and homology information


ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / IgG binding / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex ...ROBO receptors bind AKAP5 / cAMP-dependent protein kinase regulator activity / negative regulation of cAMP-dependent protein kinase activity / nucleotide-activated protein kinase complex / IgG binding / cAMP-dependent protein kinase inhibitor activity / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / ciliary base / cAMP-dependent protein kinase complex / plasma membrane raft / protein kinase A catalytic subunit binding / PKA activation in glucagon signalling / DARPP-32 events / Hedgehog 'off' state / cAMP binding / FCGR3A-mediated IL10 synthesis / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / intracellular signal transduction / protein domain specific binding / focal adhesion / centrosome / ubiquitin protein ligase binding / protein-containing complex / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily ...cAMP-dependent protein kinase regulatory subunit / cAMP-dependent protein kinase regulatory subunit, dimerization-anchoring domain / Regulatory subunit of type II PKA R-subunit / RIIalpha, Regulatory subunit portion of type II PKA R-subunit / Octapeptide repeat / Octapeptide repeat / Protein A, Ig-binding domain / B domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Gram-positive cocci surface proteins LPxTG motif profile. / Cyclic nucleotide-binding domain superfamily / LPXTG cell wall anchor domain / RmlC-like jelly roll fold
Similarity search - Domain/homology
cAMP-dependent protein kinase type II-alpha regulatory subunit / Immunoglobulin G-binding protein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsYoun, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Lee, H. / Lee, J.O.
CitationJournal: Sci Rep / Year: 2017
Title: Construction of novel repeat proteins with rigid and predictable structures using a shared helix method.
Authors: Youn, S.J. / Kwon, N.Y. / Lee, J.H. / Kim, J.H. / Choi, J. / Lee, H. / Lee, J.O.
History
DepositionMar 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
C: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
D: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)44,5224
Polymers44,5224
Non-polymers00
Water00
1
A: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
B: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)22,2612
Polymers22,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-20 kcal/mol
Surface area8780 Å2
MethodPISA
2
C: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A
D: cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A


Theoretical massNumber of molelcules
Total (without water)22,2612
Polymers22,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-20 kcal/mol
Surface area12120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.988, 174.147, 103.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEGLUGLUAA5 - 416 - 42
21ILEILEGLUGLUBB5 - 416 - 42
12ILEILEGLUGLUAA5 - 416 - 42
22ILEILEGLUGLUCC5 - 416 - 42
13ILEILEGLUGLUAA5 - 416 - 42
23ILEILEGLUGLUDD5 - 416 - 42
14ILEILEGLNGLNBB5 - 936 - 94
24ILEILEGLNGLNCC5 - 936 - 94
15TRPTRPGLNGLNBB3 - 934 - 94
25TRPTRPGLNGLNDD3 - 934 - 94
16ILEILEGLNGLNCC5 - 936 - 94
26ILEILEGLNGLNDD5 - 936 - 94

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Antibody
cAMP-dependent protein kinase type II-alpha regulatory subunit,Immunoglobulin G-binding protein A / IgG-binding protein A / Staphylococcal protein A


Mass: 11130.393 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 5-44,UNP RESIDUES 217-269 / Mutation: G240A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of 4 tags, PKA (UNP residues 5-44) and Protein A (UNP residues 217-269)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Staphylococcus aureus (bacteria)
Gene: PRKAR2A, PKR2, PRKAR2, spa / Production host: Escherichia coli (E. coli) / References: UniProt: P13861, UniProt: P38507

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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: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8.5 / Details: 100mM Tris pH 8.5, 2.16M Sodium formate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 10889 / % possible obs: 98.9 % / Redundancy: 6.3 % / Net I/σ(I): 23.6
Reflection shellResolution: 3.3→3.42 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IZX, 4ZNC

2izx

4znc


Resolution: 3.25→43.537 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.871 / SU B: 75.516 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.509 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30675 541 5 %RANDOM
Rwork0.25076 ---
obs0.25359 10339 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 165.823 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å2-0 Å20 Å2
2---11.1 Å2-0 Å2
3---7.64 Å2
Refinement stepCycle: 1 / Resolution: 3.25→43.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 0 0 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.9763538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9655309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18425.57149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.30815447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8291518
X-RAY DIFFRACTIONr_chiral_restr0.1090.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212042
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_it9.8627.5841248
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it13.67611.351553
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it13.0557.7251351
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined18.64610357
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.0232599
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded39.61952553
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A21620.16
12B21620.16
21A23220.13
22C23220.13
31A21940.15
32D21940.15
41B52900.17
42C52900.17
51B56760.12
52D56760.12
61C52440.17
62D52440.17
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.41 33 -
Rwork0.38 605 -
obs--76.87 %
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)
115.2426-2.75112.3097.9566-0.04713.38630.40260.62750.9992-0.3539-0.3185-0.789-0.21820.4602-0.08410.3121-0.06010.05740.31210.00780.1326-74.2433182.39516.1327
23.89525.1229-1.933910.8447-0.64563.3859-0.0085-0.3880.26570.525-0.30211.73710.3027-0.76910.31060.51580.16910.07310.85870.13390.5372-88.0638168.43711.6855
32.06950.40090.59990.82020.05890.1961-0.33170.89680.4195-0.20570.2149-0.6321-0.07040.36160.11681.23-0.08640.09221.0745-0.12541.0676-67.4827205.7928-9.9174
47.5923-4.5248-2.37873.34151.80520.9849-0.2058-0.96840.48450.0530.04990.3673-0.0202-0.0590.15591.6240.21350.13161.11940.02241.2831-95.4281207.03498.6409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 23
2X-RAY DIFFRACTION1A24 - 42
3X-RAY DIFFRACTION2B2 - 27
4X-RAY DIFFRACTION2B28 - 56
5X-RAY DIFFRACTION2B57 - 94
6X-RAY DIFFRACTION3C5 - 56
7X-RAY DIFFRACTION3C57 - 94
8X-RAY DIFFRACTION4D3 - 27
9X-RAY DIFFRACTION4D28 - 94

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