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- PDB-7my4: Crystal Structure of the SPA17 Docking and Dimerization Domain fr... -

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Basic information

Entry
Database: PDB / ID: 7my4
TitleCrystal Structure of the SPA17 Docking and Dimerization Domain from Danio rerio
ComponentsSperm autoantigenic protein 17
KeywordsPROTEIN BINDING / Oligomerization / A-Kinase Anchoring Protein (AKAP) Binding Domain
Function / homology
Function and homology information


cilium movement / motile cilium / calmodulin binding
Similarity search - Function
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 / IQ calmodulin-binding motif / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif profile. / IQ motif, EF-hand binding site
Similarity search - Domain/homology
Sperm autoantigenic protein 17
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsDahlin, H.R. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK119192 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Beyond PKA: Evolutionary and structural insights that define a docking and dimerization domain superfamily.
Authors: Dahlin, H.R. / Zheng, N. / Scott, J.D.
History
DepositionMay 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 11, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.title ..._citation.journal_volume / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sperm autoantigenic protein 17
B: Sperm autoantigenic protein 17
C: Sperm autoantigenic protein 17
D: Sperm autoantigenic protein 17


Theoretical massNumber of molelcules
Total (without water)33,6544
Polymers33,6544
Non-polymers00
Water6,035335
1
A: Sperm autoantigenic protein 17


Theoretical massNumber of molelcules
Total (without water)8,4131
Polymers8,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sperm autoantigenic protein 17


Theoretical massNumber of molelcules
Total (without water)8,4131
Polymers8,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sperm autoantigenic protein 17


Theoretical massNumber of molelcules
Total (without water)8,4131
Polymers8,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sperm autoantigenic protein 17


Theoretical massNumber of molelcules
Total (without water)8,4131
Polymers8,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.957, 60.957, 89.021
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Space group name HallP32
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 7 and (name N or name...
d_2ens_1(chain "B" and ((resid 7 and (name N or name...
d_3ens_1(chain "C" and ((resid 7 and (name N or name...
d_4ens_1(chain "D" and ((resid 7 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASNARGA1 - 19
d_12ens_1VALARGA22 - 24
d_13ens_1GLNTHRA27 - 40
d_14ens_1LEUARGA43 - 47
d_15ens_1GLUGLUA50
d_16ens_1GLYLEUA53 - 63
d_17ens_1ASPHISA66 - 72
d_21ens_1ASNARGB1 - 19
d_22ens_1VALARGB21 - 23
d_23ens_1GLNTHRB26 - 39
d_24ens_1LEUARGB42 - 46
d_25ens_1GLUGLUB49
d_26ens_1GLYLEUB52 - 62
d_27ens_1ASPHISB64 - 70
d_31ens_1ASNARGC1 - 19
d_32ens_1VALARGC22 - 24
d_33ens_1GLNTHRC27 - 40
d_34ens_1LEUARGC43 - 47
d_35ens_1GLUGLUC49
d_36ens_1GLYLEUC52 - 62
d_37ens_1ASPHISC64 - 70
d_41ens_1ASNARGD1 - 19
d_42ens_1VALARGD21 - 23
d_43ens_1GLNTHRD26 - 39
d_44ens_1LEUARGD42 - 46
d_45ens_1GLUGLUD48
d_46ens_1GLYLEUD51 - 61
d_47ens_1ASPHISD63 - 69

NCS oper:
IDCodeMatrixVector
1given(-0.999998882618, 0.000704253608404, 0.00131863171406), (-0.000703990370128, -0.999999732182, 0.000200083379915), (0.00131877227035, 0.000199154852317, 0.999999110588)-0.0578942959754, -0.0118158667267, 0.0403923561814
2given(0.500770104026, 0.86558032711, 1.52871988589E-5), (0.865580253336, -0.50077005389, -0.000422092065013), (-0.000357699216309, 0.000224603384766, -0.999999910802)-0.000955164013476, 0.00753663953879, 75.8187853159
3given(-0.50046378046, -0.865757382272, -0.000399361235345), (-0.865757353907, 0.500463900924, -0.000296693241964), (0.000456730246219, 0.000197265704855, -0.999999876242)0.0158138084175, 0.0075635677641, 75.8382951329

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Components

#1: Protein
Sperm autoantigenic protein 17


Mass: 8413.407 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: spa17 / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: F1QK17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.5 M magnesium formate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→34.03 Å / Num. obs: 38456 / % possible obs: 98.5 % / Redundancy: 7.6 % / Biso Wilson estimate: 11.79 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.035 / Rrim(I) all: 0.098 / Net I/σ(I): 1.02
Reflection shellResolution: 1.72→1.77 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.269 / Num. unique obs: 2519 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2izx

2izx


Resolution: 1.72→34.03 Å / SU ML: 0.1278 / Cross valid method: FREE R-VALUE / σ(F): 0.23 / Phase error: 17.0526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1645 1971 5.13 %
Rwork0.1545 36485 -
obs0.1551 38456 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 1.72→34.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 0 335 2491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00842362
X-RAY DIFFRACTIONf_angle_d0.92283219
X-RAY DIFFRACTIONf_chiral_restr0.0477329
X-RAY DIFFRACTIONf_plane_restr0.0064447
X-RAY DIFFRACTIONf_dihedral_angle_d18.5527897
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.325031633034
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.359911891657
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.333251414717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.770.17181370.17292519X-RAY DIFFRACTION94.59
1.77-1.810.20961420.16312502X-RAY DIFFRACTION95.97
1.81-1.870.16041400.15722590X-RAY DIFFRACTION97.15
1.87-1.930.19621440.15492587X-RAY DIFFRACTION98.24
1.93-20.22791410.15462630X-RAY DIFFRACTION98.68
2-2.080.1571310.14672633X-RAY DIFFRACTION99.07
2.08-2.170.15431390.13922621X-RAY DIFFRACTION99.21
2.17-2.290.16071500.14912630X-RAY DIFFRACTION98.97
2.29-2.430.11451440.14242584X-RAY DIFFRACTION99.16
2.43-2.620.19741440.14722646X-RAY DIFFRACTION99.39
2.62-2.880.19141350.15292649X-RAY DIFFRACTION99.29
2.88-3.30.14831380.15952638X-RAY DIFFRACTION99.71
3.3-4.150.15361380.14512636X-RAY DIFFRACTION99.78
4.15-34.030.15641480.17832620X-RAY DIFFRACTION99.18
Refinement TLS params.Method: refined / Origin x: -0.210331558916 Å / Origin y: -0.200844421796 Å / Origin z: 37.8921510452 Å
111213212223313233
T0.0779259569779 Å20.0287863948042 Å2-0.00054901519883 Å2-0.0450953477277 Å20.000362971403594 Å2--0.0354127861403 Å2
L0.541648496246 °20.297926969854 °2-0.000872194938204 °2-0.200679303135 °20.00409434686855 °2--0.0572123171208 °2
S-0.00939055500169 Å °-0.00872362069306 Å °-2.46752128488E-5 Å °-0.0120779178371 Å °0.00469030002087 Å °0.00156538360692 Å °0.000140546448106 Å °-0.000648191639035 Å °0.00140446904927 Å °
Refinement TLS groupSelection details: all

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