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- PDB-3pyb: Crystal structure of ent-copalyl diphosphate synthase from Arabid... -

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Basic information

Entry
Database: PDB / ID: 3pyb
TitleCrystal structure of ent-copalyl diphosphate synthase from Arabidopsis thaliana in complex with 13-aza-13,14-dihydrocopalyl diphosphate
ComponentsEnt-copalyl diphosphate synthase, chloroplastic
KeywordsISOMERASE / class I and II terpene cyclase fold / class II diterpene cyclase / DXXDD motif / gibberellin biosynthesis / Biosynthesis of ent-copalyl diphosphate
Function / homology
Function and homology information


ent-copalyl diphosphate synthase / ent-copalyl diphosphate synthase activity / gibberellin biosynthetic process / gibberellic acid mediated signaling pathway / terpene synthase activity / chloroplast / magnesium ion binding
Similarity search - Function
Glycosyltransferase - #160 / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Glycosyltransferase - #160 / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-A3C / Ent-copalyl diphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.759 Å
AuthorsKoksal, M. / Christianson, D.W.
CitationJournal: To be Published
Title: Structure of ent-Copalyl Diphosphate Synthase from Arabidopsis thaliana, a Protonation-Dependent Diterpene Cyclase
Authors: Koksal, M. / Hu, H. / Coates, R.M. / Peters, R.J. / Christianson, D.W.
History
DepositionDec 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / 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 / _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: Ent-copalyl diphosphate synthase, chloroplastic
B: Ent-copalyl diphosphate synthase, chloroplastic
C: Ent-copalyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,11913
Polymers254,5213
Non-polymers2,59810
Water3,621201
1
A: Ent-copalyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2476
Polymers84,8401
Non-polymers1,4075
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ent-copalyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5554
Polymers84,8401
Non-polymers7153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ent-copalyl diphosphate synthase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3173
Polymers84,8401
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.738, 188.554, 229.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ent-copalyl diphosphate synthase, chloroplastic / AtCPS / Ent-CDP synthase / Ent-kaurene synthase A / KSA


Mass: 84840.266 Da / Num. of mol.: 3 / Fragment: ent-Copalyl Diphosphate Synthase
Source method: isolated from a genetically manipulated source
Details: vector: pET22bTV is a derivative of pET22b / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g02780, GA1, T5J8.9, TPSGA1 / Plasmid: pET22bCV / Production host: Escherichia coli (E. coli) / Strain (production host): OverExpress C41 (DE3)
References: UniProt: Q38802, ent-copalyl diphosphate synthase
#2: Chemical ChemComp-A3C / 2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate / 13-aza-13,14-dihydrocopalyl diphosphate


Mass: 453.447 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H37NO7P2
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 100 mM sodium citrate (pH 5.4), 30 % polyethylene glycol 400, 200 mM KH2PO4, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2010 / Details: Kirpatrick Baez focusing mirrors
RadiationMonochromator: Si(111) double crystal monochromator (Kohzu HLD8-24 Monochromator)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. all: 67547 / Num. obs: 67547 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 12
Reflection shellResolution: 2.75→2.85 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.227 / Num. unique all: 6022 / Rsym value: 0.768 / % possible all: 86.1

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Processing

Software
NameVersionClassification
APS24IDC Softwaredata collection
PHENIX(PHASER)model building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX(PHASER)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PYA

3pya


Resolution: 2.759→44.519 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 1842 2.96 %RANDOM
Rwork0.1766 ---
all0.1789 67547 --
obs0.1789 62150 86.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.336 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-21.8872 Å2-0 Å2-0 Å2
2---15.6954 Å20 Å2
3----6.1918 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.759→44.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16855 0 173 201 17229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417475
X-RAY DIFFRACTIONf_angle_d0.78223572
X-RAY DIFFRACTIONf_dihedral_angle_d19.9826402
X-RAY DIFFRACTIONf_chiral_restr0.0572476
X-RAY DIFFRACTIONf_plane_restr0.0033002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7588-2.83340.3349800.22682807X-RAY DIFFRACTION53
2.8334-2.91670.35291150.22643658X-RAY DIFFRACTION69
2.9167-3.01080.32211180.22423898X-RAY DIFFRACTION73
3.0108-3.11840.35381320.21874114X-RAY DIFFRACTION78
3.1184-3.24330.34081350.20734310X-RAY DIFFRACTION81
3.2433-3.39080.29641350.18794605X-RAY DIFFRACTION86
3.3908-3.56950.26551520.16854875X-RAY DIFFRACTION91
3.5695-3.7930.24321560.14885111X-RAY DIFFRACTION96
3.793-4.08570.2051560.14285178X-RAY DIFFRACTION96
4.0857-4.49650.21831600.13385298X-RAY DIFFRACTION98
4.4965-5.14640.23441630.13155322X-RAY DIFFRACTION98
5.1464-6.48070.24161670.16545443X-RAY DIFFRACTION99
6.4807-44.52470.22251730.18925689X-RAY DIFFRACTION99

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