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- PDB-2r2i: Myristoylated Guanylate Cyclase Activating Protein-1 with Calcium... -

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Basic information

Entry
Database: PDB / ID: 2r2i
TitleMyristoylated Guanylate Cyclase Activating Protein-1 with Calcium Bound
ComponentsGuanylyl cyclase-activating protein 1
KeywordsLyase Activator / EF hand / GCAP / Guanylate Cyclase Activating Protein / GCAP1 / GCAP-1 / Calcium / Lipoprotein / Myristate / Sensory transduction / Vision
Function / homology
Function and homology information


Inactivation, recovery and regulation of the phototransduction cascade / guanylate cyclase regulator activity / cone photoreceptor outer segment / calcium sensitive guanylate cyclase activator activity / positive regulation of guanylate cyclase activity / phototransduction / photoreceptor inner segment / cellular response to calcium ion / visual perception / calcium ion binding
Similarity search - Function
Recoverin family / EF hand / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...Recoverin family / EF hand / EF-hand domain pair / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / MYRISTIC ACID / Guanylyl cyclase-activating protein 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsStephen, R.
CitationJournal: Structure / Year: 2007
Title: Stabilizing function for myristoyl group revealed by the crystal structure of a neuronal calcium sensor, guanylate cyclase-activating protein 1.
Authors: Stephen, R. / Bereta, G. / Golczak, M. / Palczewski, K. / Sousa, M.C.
History
DepositionAug 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Guanylyl cyclase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3929
Polymers22,7311
Non-polymers6618
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.333, 73.333, 73.229
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Guanylyl cyclase-activating protein 1 / GCAP 1 / Guanylate cyclase activator 1A


Mass: 22730.703 Da / Num. of mol.: 1 / Fragment: Guanylate Cyclase Activating Protein-1 / Mutation: G6S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: GUCA1A, GCAP1 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P79880
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2
#4: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1743.2
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop6.524% PEG 20,000, 0.4 M potassium nitrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop81.8 M ammonium sulfate, 0.1 M Tris-chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211.5498
SYNCHROTRONALS 8.3.121.3856, 1.3862, 1.3122
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJun 7, 2004
ADSC QUANTUM 3152CCDNov 16, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal, Si(111)SINGLE WAVELENGTHMx-ray1
2Double flat crystal, Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54981
21.38561
31.38621
41.31221
ReflectionResolution: 2→50 Å / Num. all: 14065 / Num. obs: 13602 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 15.6 Å2
Reflection shellResolution: 2→2.07 Å / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementResolution: 2→29.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 93709.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1357 10.1 %RANDOM
Rwork0.218 ---
obs0.218 13373 95.3 %-
all-14019 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.089 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1480 0 34 84 1598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 203 9.4 %
Rwork0.217 1953 -
all-2156 -
obs--95.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3myr.parammyr.top
X-RAY DIFFRACTION4bme.parambme.top
X-RAY DIFFRACTION5water.paramwater.top

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