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- PDB-4rj9: Structure of a plant specific C2 domain protein, OsGAP1 from rice -

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Basic information

Entry
Database: PDB / ID: 4rj9
TitleStructure of a plant specific C2 domain protein, OsGAP1 from rice
ComponentsC2 domain-containing protein-like
KeywordsLIGASE / Beta_sandwich / Lipid selectivity / calcium-dependent / phospholipid binding / membrane targeting / Cytosol
Function / homology
Function and homology information


positive regulation of defense response to bacterium => GO:1900426 / positive regulation of response to salt stress / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / defense response / response to wounding / lipid binding / nucleus ...positive regulation of defense response to bacterium => GO:1900426 / positive regulation of response to salt stress / abscisic acid-activated signaling pathway / response to salt stress / GTPase activator activity / positive regulation of GTPase activity / defense response / response to wounding / lipid binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile.
Similarity search - Domain/homology
: / GTPase activating protein 1
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMiao, R. / Fong, Y.H. / Wong, K.B. / Lam, H.M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Site-directed Mutagenesis Shows the Significance of Interactions with Phospholipids and the G-protein OsYchF1 for the Physiological Functions of the Rice GTPase-activating Protein 1 (OsGAP1).
Authors: Yung, Y.L. / Cheung, M.Y. / Miao, R. / Fong, Y.H. / Li, K.P. / Yu, M.H. / Chye, M.L. / Wong, K.B. / Lam, H.M.
History
DepositionOct 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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: C2 domain-containing protein-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6523
Polymers18,5741
Non-polymers782
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.190, 166.750, 60.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein C2 domain-containing protein-like / G-protein binding protein / Os02g0327000 protein / cDNA clone:006-212-C07 / full insert sequence / ...G-protein binding protein / Os02g0327000 protein / cDNA clone:006-212-C07 / full insert sequence / cDNA clone:J033052D22 / full insert sequence


Mass: 18573.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os02g0327000, OsGAP1, OSJNBb0042G06.10, OsJ_06508, P0476C12.36
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6YWF1, DNA ligase (ATP)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.53 Å3/Da / Density % sol: 51.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Potassium sodium tartrate terrahydrate and 20% w/v PEG3350, pH 8.4-9.1, VAPOR DIFFUSION, SITTING DROP, temperature 289K
PH range: 8.4-9.1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 30, 2011
RadiationMonochromator: graded multilayer monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→30.37 Å / Num. all: 23481 / Num. obs: 23481 / % possible obs: 98.1 % / Observed criterion σ(F): 12.3 / Observed criterion σ(I): 5 / Redundancy: 6.9 % / Rmerge(I) obs: 0.106 / Rsym value: 0.307
Reflection shellResolution: 1.63→30.37 Å / % possible all: 98

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_650)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CM6

2cm6


Resolution: 1.63→30.365 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 18.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1998 8.36 %
Rwork0.183 --
obs0.1847 23481 98.64 %
all-23481 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6414 Å2-0 Å20 Å2
2---6.097 Å2-0 Å2
3---4.4556 Å2
Refinement stepCycle: LAST / Resolution: 1.63→30.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1269 0 2 277 1548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071283
X-RAY DIFFRACTIONf_angle_d1.2141737
X-RAY DIFFRACTIONf_dihedral_angle_d13.911502
X-RAY DIFFRACTIONf_chiral_restr0.05211
X-RAY DIFFRACTIONf_plane_restr0.005222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.66870.23331370.19011494X-RAY DIFFRACTION97
1.6687-1.71380.22561390.17791522X-RAY DIFFRACTION97
1.7138-1.76420.1991390.17791524X-RAY DIFFRACTION97
1.7642-1.82120.19181380.17231512X-RAY DIFFRACTION98
1.8212-1.88630.24011390.18621542X-RAY DIFFRACTION98
1.8863-1.96180.22761410.18821544X-RAY DIFFRACTION98
1.9618-2.0510.22021420.17471555X-RAY DIFFRACTION99
2.051-2.15910.1971410.1711543X-RAY DIFFRACTION99
2.1591-2.29440.20421420.18281558X-RAY DIFFRACTION99
2.2944-2.47140.22811440.19631579X-RAY DIFFRACTION100
2.4714-2.720.21621450.19771586X-RAY DIFFRACTION100
2.72-3.11330.21091470.19671600X-RAY DIFFRACTION100
3.1133-3.92110.19521480.17281622X-RAY DIFFRACTION100
3.9211-30.37030.17381560.17911715X-RAY DIFFRACTION100

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