5GWP

Crystal structure of RCAR3:PP2C wild-type with (+)-ABA

> Summary

Summary for 5GWP

Related5GWO
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 weight111811.22
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 (2.577 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.244600.4%2.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

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

More Biological unit images

Molmil generated image of 5gwp
no rotation
Molmil generated image of 5gwp
rotated about x axis by 90°
Molmil generated image of 5gwp
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 (5gwp.pdb1.gz [155.52 KB])
Coordinate files for Biological unit (5gwp.pdb2.gz [151.48 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BProbable protein phosphatase 2C 50polymer32735507.52
UniProt (Q6L5H6)
Pfam (PF00481)
Oryza sativa subsp. japonica (Rice)OsPP2C50
C, DABA receptor RCAR3polymer17520060.92
UniProt (K4N2F7)
Pfam (PF10604)
Oryza sativa (Rice)
MAGNESIUM IONnon-polymer24.36
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acidnon-polymer264.32
waterwater18.078

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight111136.8
Non-Polymers*Number of molecules8
Total molecular weight674.5
All*Total molecular weight111811.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.577 Å)

Cell axes74.981133.684191.279
Cell angles90.0090.0090.00
SpacegroupC 2 2 21
Resolution limits46.14 - 2.58
the highest resolution shell value2.642 - 2.578
R-factor0.2087
R-work0.20600
the highest resolution shell value0.258
R-free0.24670
the highest resolution shell value0.322
RMSD bond length0.002
RMSD bond angle0.519

Data Collection Statistics

Resolution limits46.14 - 2.58
the highest resolution shell value -
Number of reflections30728
Rmerge_l_obs0.114
Completeness96.0
Redundancy11

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6295

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
AC16binding site for residue MG A 401
ChainResidue
AASP118
AASP306
AASP368
AHOH505
AHOH509
AHOH520

AC23binding site for residue MG A 402
ChainResidue
AASP306
AASP310
AHOH516

AC36binding site for residue MG A 403
ChainResidue
AASP118
AGLY119
AHOH502
AHOH503
AHOH520
AHOH530

AC46binding site for residue MG B 401
ChainResidue
BASP118
BASP306
BASP368
BHOH511
BHOH513
BHOH524

AC54binding site for residue MG B 402
ChainResidue
BASP306
BASP310
BHOH509
BHOH520

AC66binding site for residue MG B 403
ChainResidue
BASP118
BGLY119
BHOH504
BHOH513
BHOH514
BHOH526

AC710binding site for residue A8S C 301
ChainResidue
CLYS76
CVAL98
CALA104
CPHE125
CPHE174
CLEU178
CASN182
CHOH406
CHOH407
CHOH411

AC87binding site for residue A8S D 301
ChainResidue
DLYS76
DSER107
DPHE125
DHIS130
DLEU178
DASN182
DHOH404

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

site_idNumber of ResiduesDetails
A8S_5gwp_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_5gwp_D_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
BTRP259A8S: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
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)
PDBallpdb5gwp.ent.gz (309.03 KB)
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all (no-compress)pdb5gwp.ent (1.19 MB)
header onlypdb5gwp.ent.gz (9.42 KB)
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PDBx/mmCIF5gwp.cif.gz (364.26 KB)
PDBMLall5gwp.xml.gz (509.01 KB)
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no-atom5gwp-noatom.xml.gz (37.77 KB)
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ext-atom5gwp-extatom.xml.gz (164.44 KB)
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PDBMLplusall5gwp-plus.xml.gz (511.05 KB)
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no-atom5gwp-plus-noatom.xml.gz (39.8 KB)
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add only5gwp-add.xml.gz (2.03 KB)
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RDF5gwp.rdf.gz (84.02 KB)
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Structure factorsr5gwpsf.ent.gz (342.2 KB)
Biological unit (PDB format)5gwp.pdb1.gz (155.52 KB) (A,C)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5gwp.pdb2.gz (151.48 KB) (B,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5gwp​_validation.pdf.gz (296.29 KB)
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PDF-full5gwp​_full​_validation.pdf.gz (304.8 KB)
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XML5gwp​_validation.xml.gz (32.62 KB)
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PNG5gwp​_multipercentile​_validation.png.gz (156.46 KB)
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SVG5gwp​_multipercentile​_validation.svg.gz (925 B)
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Sequence (fasta)5gwp​_seq.txt
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