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- PDB-5ie3: Crystal structure of a plant enzyme -

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Basic information

Entry
Database: PDB / ID: 5ie3
TitleCrystal structure of a plant enzyme
ComponentsOxalate--CoA ligase
KeywordsLIGASE / Arabidopsis / Oxalate degradation
Function / homology
Function and homology information


seed coat development / oxalate-CoA ligase / oxalate-CoA ligase activity / positive regulation of seed germination / oxalate catabolic process / apoplast / plasmodesma / chloroplast stroma / defense response to fungus / chloroplast ...seed coat development / oxalate-CoA ligase / oxalate-CoA ligase activity / positive regulation of seed germination / oxalate catabolic process / apoplast / plasmodesma / chloroplast stroma / defense response to fungus / chloroplast / ATP binding / cytoplasm / cytosol
Similarity search - Function
Oxalate--CoA ligase Pcs60-like / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / OXALIC ACID / Oxalate--CoA ligase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFan, M.R. / Li, M. / Chang, W.R.
CitationJournal: Mol Plant / Year: 2016
Title: Crystal Structures of Arabidopsis thaliana Oxalyl-CoA Synthetase Essential for Oxalate Degradation
Authors: Fan, M. / Xiao, Y. / Li, M. / Chang, W.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxalate--CoA ligase
B: Oxalate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1016
Polymers111,2262
Non-polymers8754
Water21,5641197
1
A: Oxalate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0503
Polymers55,6131
Non-polymers4372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-4 kcal/mol
Surface area20640 Å2
MethodPISA
2
B: Oxalate--CoA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0503
Polymers55,6131
Non-polymers4372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-3 kcal/mol
Surface area20480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.193, 117.043, 72.062
Angle α, β, γ (deg.)90.00, 93.59, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Oxalate--CoA ligase / 4-coumarate--CoA ligase isoform 8 / At4CL8 / 4-coumarate--CoA ligase-like 10 / Acyl-activating ...4-coumarate--CoA ligase isoform 8 / At4CL8 / 4-coumarate--CoA ligase-like 10 / Acyl-activating enzyme 3 / Adenosine monophosphate binding protein 3 / AtMPBP3 / Oxalyl-CoA synthetase


Mass: 55613.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AAE3, 4CLL10, AMPBP3, At3g48990, T2J13.170 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SMT7, oxalate-CoA ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1197 / 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: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.6
Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic (pH 5.6), 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.84178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.84178 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 89721 / % possible obs: 96.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 15.6
Reflection shellResolution: 1.9→27.45 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→27.455 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.95
RfactorNum. reflection% reflection
Rfree0.206 1960 2.19 %
Rwork0.1601 --
obs0.1611 89438 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→27.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7686 0 58 1197 8941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147951
X-RAY DIFFRACTIONf_angle_d1.33210823
X-RAY DIFFRACTIONf_dihedral_angle_d14.2592921
X-RAY DIFFRACTIONf_chiral_restr0.071251
X-RAY DIFFRACTIONf_plane_restr0.0071397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8967-1.94410.35061030.28485025X-RAY DIFFRACTION78
1.9441-1.99670.28811400.22495931X-RAY DIFFRACTION91
1.9967-2.05540.28951360.18656462X-RAY DIFFRACTION100
2.0554-2.12170.21181540.17846464X-RAY DIFFRACTION100
2.1217-2.19750.21261380.17466450X-RAY DIFFRACTION100
2.1975-2.28550.21931530.17296478X-RAY DIFFRACTION99
2.2855-2.38940.23041390.1746410X-RAY DIFFRACTION99
2.3894-2.51530.27611360.17786355X-RAY DIFFRACTION98
2.5153-2.67280.25931480.18556296X-RAY DIFFRACTION97
2.6728-2.87890.26441480.17816221X-RAY DIFFRACTION96
2.8789-3.16830.19141430.16786171X-RAY DIFFRACTION95
3.1683-3.62590.18121400.13926217X-RAY DIFFRACTION95
3.6259-4.56480.15971450.12256402X-RAY DIFFRACTION98
4.5648-27.45760.15131370.13746596X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 2.5585 Å / Origin y: -7.0843 Å / Origin z: 71.7415 Å
111213212223313233
T0.1532 Å2-0.0082 Å2-0.0177 Å2-0.1262 Å20.0089 Å2--0.1344 Å2
L0.4415 °2-0.1326 °2-0.1054 °2-0.2435 °20.0785 °2--0.1951 °2
S-0.0127 Å °-0.0196 Å °0.0249 Å °0.0036 Å °0.0056 Å °-0.0079 Å °-0.0056 Å °0.0208 Å °0.0055 Å °
Refinement TLS groupSelection details: all

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