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- PDB-2ggz: Crystal Structure of Human Guanylate Cyclase Activating Protein-3 -

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Basic information

Entry
Database: PDB / ID: 2ggz
TitleCrystal Structure of Human Guanylate Cyclase Activating Protein-3
ComponentsGuanylyl cyclase-activating protein 3
KeywordsLYASE ACTIVATOR / EF hand / Guanylate Cyclase Activating Protein / GCAP / GCAP3 / GCAP-3
Function / homology
Function and homology information


calcium sensitive guanylate cyclase activator activity / regulation of opsin-mediated signaling pathway / visual perception / photoreceptor disc membrane / Inactivation, recovery and regulation of the phototransduction cascade / calcium ion binding / signal transduction
Similarity search - Function
Guanylyl cyclase-activating protein 3 / Recoverin family / EF hand / 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. ...Guanylyl cyclase-activating protein 3 / Recoverin family / EF hand / 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
Guanylyl cyclase-activating protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsStephen, R.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of GCAP3 Suggests Molecular Mechanism of GCAP-linked Cone Dystrophies.
Authors: Stephen, R. / Palczewski, K. / Sousa, M.C.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 3
B: Guanylyl cyclase-activating protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3278
Polymers48,0872
Non-polymers2406
Water00
1
A: Guanylyl cyclase-activating protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1644
Polymers24,0431
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Guanylyl cyclase-activating protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1644
Polymers24,0431
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.190, 88.190, 71.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Guanylyl cyclase-activating protein 3 / GCAP 3 / Guanylate cyclase activator 1C


Mass: 24043.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMS261 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O95843
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca

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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 (%)
12.9157.77
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2891vapor diffusion, hanging drop6.50.1 M MES, 5% PEG 6000, 5% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
2892vapor diffusion, hanging drop70.1 M HEPES, 5% PEG 6000, 5% MPD, pH 7.0, 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 5.0.311
SYNCHROTRONALS 8.2.120.97954, 0.97969, 0.96430
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 1, 2004
ADSC QUANTUM 2102CCDDec 20, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979541
30.979691
40.96431
ReflectionResolution: 3→25 Å / Num. all: 11042 / Num. obs: 10427 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3→3.11 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3→23.43 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 935376.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 547 5.2 %RANDOM
Rwork0.256 ---
obs0.256 10425 94.5 %-
all-11032 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9432 Å2 / ksol: 0.320635 e/Å3
Displacement parametersBiso mean: 68.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.35 Å20 Å20 Å2
2--12.35 Å20 Å2
3----24.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 3→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 6 0 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.772
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.498 96 5.5 %
Rwork0.396 1657 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param

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