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- PDB-9b99: Crystal structure of Grindelia robusta 7,13-copalyl diphosphate s... -

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Basic information

Entry
Database: PDB / ID: 9b99
TitleCrystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase
ComponentsLabda-7,13E-dienyl diphosphate synthase
KeywordsPLANT PROTEIN / Terpene synthases Class II Diterpene synthases
Function / homology
Function and homology information


terpene synthase activity / magnesium ion binding
Similarity search - Function
Terpene synthase, metal-binding 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 / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Labda-7,13E-dienyl diphosphate synthase
Similarity search - Component
Biological speciesGrindelia hirsutula (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsPereira, J.H. / Cowie, A.E. / Zerbe, P. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The crystal structure of Grindelia robusta 7,13-copalyl diphosphate synthase reveals active site features controlling catalytic specificity.
Authors: Cowie, A.E. / Pereira, J.H. / DeGiovanni, A. / McAndrew, R.P. / Palayam, M. / Peek, J.O. / Muchlinski, A.J. / Yoshikuni, Y. / Shabek, N. / Adams, P.D. / Zerbe, P.
History
DepositionApr 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Labda-7,13E-dienyl diphosphate synthase


Theoretical massNumber of molelcules
Total (without water)84,7281
Polymers84,7281
Non-polymers00
Water5,477304
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.070, 79.110, 88.440
Angle α, β, γ (deg.)90.000, 97.590, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Labda-7,13E-dienyl diphosphate synthase


Mass: 84727.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Grindelia hirsutula (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H4SRM2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate 0.1 M Tris pH 8.5 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.12→58.73 Å / Num. obs: 43361 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.05 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.2
Reflection shellResolution: 2.12→2.16 Å / Num. unique obs: 4322 / CC1/2: 0.566

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→58.73 Å / SU ML: 0.2382 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.208
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.229 2178 5.02 %
Rwork0.1852 41183 -
obs0.1874 43361 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.51 Å2
Refinement stepCycle: LAST / Resolution: 2.12→58.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5790 0 0 304 6094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00345943
X-RAY DIFFRACTIONf_angle_d0.52688054
X-RAY DIFFRACTIONf_chiral_restr0.0339881
X-RAY DIFFRACTIONf_plane_restr0.01541016
X-RAY DIFFRACTIONf_dihedral_angle_d16.28792176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.170.33161420.28372564X-RAY DIFFRACTION99.56
2.17-2.220.27811390.25162560X-RAY DIFFRACTION99.16
2.22-2.270.27461300.23872546X-RAY DIFFRACTION99.7
2.27-2.330.26221380.23292582X-RAY DIFFRACTION99.34
2.33-2.40.29491390.22572536X-RAY DIFFRACTION99.59
2.4-2.480.27341470.22562563X-RAY DIFFRACTION99.41
2.48-2.570.27061180.21082587X-RAY DIFFRACTION99.59
2.57-2.670.26981420.20542562X-RAY DIFFRACTION99.41
2.67-2.790.25731350.1942556X-RAY DIFFRACTION99.52
2.79-2.940.21841420.19742578X-RAY DIFFRACTION99.71
2.94-3.120.27961420.20872576X-RAY DIFFRACTION99.71
3.12-3.370.23631400.19122555X-RAY DIFFRACTION99.63
3.37-3.70.20251280.16482609X-RAY DIFFRACTION99.35
3.7-4.240.17621300.14672550X-RAY DIFFRACTION98.46
4.24-5.340.17871370.1392592X-RAY DIFFRACTION99.34
5.34-58.730.20871290.17562667X-RAY DIFFRACTION99.57

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