5GWO

Crystal structure of RCAR3:PP2C S265F/I267M with (+)-ABA

> Summary

Summary for 5GWO

Related5GWP
DescriptorProbable protein phosphatase 2C 50, ABA receptor RCAR3, MAGNESIUM ION, ... (5 entities in total)
Functional Keywordsabscisic acid, aba receptor, pp2c, hydrolase-receptor complex, hydrolase/receptor
Biological sourceOryza sativa subsp. japonica (Rice)
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Total number of polymer chains4
Total molecular weight111943.18
Authors
Han, S.,Lee, S. (deposition date: 2016-09-12, release date: 2017-09-13)
Primary citation
Han, S.,Min, M.K.,Lee, S.Y.,Lim, C.W.,Bhatnagar, N.,Lee, Y.,Shin, D.,Chung, K.Y.,Lee, S.C.,Kim, B.G.,Lee, S.
Modulation of ABA signaling by altering VxG Phi L motif of PP2Cs in Oryza sativa
Mol Plant, 2017
PubMed: 28827170 (PDB entries with the same primary citation)
DOI: 10.1016/j.molp.2017.08.003
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.816 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2441300.1%1.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5gwo
no rotation
Molmil generated image of 5gwo
rotated about x axis by 90°
Molmil generated image of 5gwo
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5gwo
no rotation
Molmil generated image of 5gwo
rotated about x axis by 90°
Molmil generated image of 5gwo
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5gwo.pdb1.gz [160.34 KB])
Coordinate files for Biological unit (5gwo.pdb2.gz [160.84 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BProbable protein phosphatase 2C 50polymer32735585.62
UniProt (Q6L5H6)
Oryza sativa subsp. japonica (Rice)OsPP2C50
C, DABA receptor RCAR3polymer17520060.92
UniProt (K4N2F7)
Oryza sativa (Rice)
MAGNESIUM IONnon-polymer24.35
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acidnon-polymer264.32
waterwater18.037

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight111293.0
Non-Polymers*Number of molecules7
Total molecular weight650.2
All*Total molecular weight111943.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.816 Å)

Cell axes46.47279.25380.288
Cell angles81.6387.0873.98
SpacegroupP 1
Resolution limits37.73 - 2.82
the highest resolution shell value2.886 - 2.816
R-factor0.1895
R-work0.18490
the highest resolution shell value0.273
R-free0.24270
the highest resolution shell value0.347
RMSD bond length0.005
RMSD bond angle0.937

Data Collection Statistics

Resolution limits37.73 - 2.82
the highest resolution shell value -
Number of reflections25506
Rmerge_l_obs0.107
Completeness97.0
Redundancy3.2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC15binding site for residue MG A 401
ChainResidue
AASP220
ALYS239
AASP306
AASP310
AHOH505

AC26binding site for residue MG A 402
ChainResidue
AASP118
AGLY119
AMG403
AHOH511
AHOH516
AHOH518

AC35binding site for residue MG A 403
ChainResidue
AASP118
AASP306
AASP368
AMG402
AHOH501

AC47binding site for residue MG B 401
ChainResidue
BASP118
BGLY119
BMG402
BHOH502
BHOH507
BHOH508
BHOH509

AC56binding site for residue MG B 402
ChainResidue
BASP118
BASP306
BASP368
BMG401
BHOH501
BHOH509

AC610binding site for residue A8S C 301
ChainResidue
CLYS76
CLEU102
CSER107
CPHE125
CPHE174
CLEU178
CASN182
CHOH401
CHOH402
CHOH404

AC710binding site for residue A8S D 301
ChainResidue
DLYS76
DLEU102
DALA104
DSER107
DPHE125
DHIS130
DLEU132
DPHE174
DLEU178
DASN182

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
A8S_5gwo_C_30120(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid binding site
ChainResidueligand
ATRP259A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CLYS76A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CPHE78A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CVAL98A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CLEU102-ALA104A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CARG106-SER107A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CGLU109A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CPHE125A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CHIS130A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CLEU132A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CTYR135A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CGLU156A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CPHE174-VAL175A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CLEU178-LEU179A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
CASN182A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

A8S_5gwo_D_30119(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid binding site
ChainResidueligand
DLYS76A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DPHE78A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DVAL98A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DLEU102-ALA104A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DARG106-SER107A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DGLU109A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DPHE125A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DHIS130A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DLEU132A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DTYR135A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DGLU156A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DPHE174-VAL175A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DLEU178-LEU179A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
DASN182A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI13Manganese 2. {ECO:0000250}
ChainResidueDetails
AASP60
AASP248
AASP310

SWS_FT_FI21Manganese 1. {ECO:0000250}
ChainResidueDetails
AASP60

SWS_FT_FI31Manganese 1; via carbonyl oxygen. {ECO:0000250}
ChainResidueDetails
AGLY61

SWS_FT_FI43Manganese 2. {ECO:0000250}
ChainResidueDetails
BASP60
BASP248
BASP310

SWS_FT_FI51Manganese 1. {ECO:0000250}
ChainResidueDetails
BASP60

SWS_FT_FI61Manganese 1; via carbonyl oxygen. {ECO:0000250}
ChainResidueDetails
BGLY61

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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5gwo.ent.gz (322.77 KB)
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all (no-compress)pdb5gwo.ent (1.23 MB)
header onlypdb5gwo.ent.gz (8.94 KB)
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PDBx/mmCIF5gwo.cif.gz (382.13 KB)
PDBMLall5gwo.xml.gz (527.82 KB)
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no-atom5gwo-noatom.xml.gz (36.26 KB)
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ext-atom5gwo-extatom.xml.gz (175.28 KB)
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PDBMLplusall5gwo-plus.xml.gz (529.43 KB)
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no-atom5gwo-plus-noatom.xml.gz (37.86 KB)
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add only5gwo-add.xml.gz (1.6 KB)
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RDF5gwo.rdf.gz (81.39 KB)
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Structure factorsr5gwosf.ent.gz (178.6 KB)
Biological unit (PDB format)5gwo.pdb1.gz (160.34 KB) (A,C)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5gwo.pdb2.gz (160.84 KB) (B,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5gwo​_validation.pdf.gz (304.85 KB)
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PDF-full5gwo​_full​_validation.pdf.gz (321.06 KB)
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XML5gwo​_validation.xml.gz (35.07 KB)
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PNG5gwo​_multipercentile​_validation.png.gz (156.72 KB)
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SVG5gwo​_multipercentile​_validation.svg.gz (931 B)
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Sequence (fasta)5gwo​_seq.txt
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