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- PDB-7s5l: Cembrene A synthase from Eleutherobia rubra -

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Basic information

Entry
Database: PDB / ID: 7s5l
TitleCembrene A synthase from Eleutherobia rubra
ComponentsCembrene A synthase
KeywordsBIOSYNTHETIC PROTEIN / terpene / diterpene synthase / octocoral / Cembrene A / Eleutherobia rubra
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesEleutherobia rubra (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsChen, P.Y.-T. / Moore, B.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM085770 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Ancient plant-like terpene biosynthesis in corals.
Authors: Burkhardt, I. / de Rond, T. / Chen, P.Y. / Moore, B.S.
History
DepositionSep 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cembrene A synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9825
Polymers45,7611
Non-polymers2224
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint1 kcal/mol
Surface area16610 Å2
Unit cell
Length a, b, c (Å)85.689, 101.649, 46.342
Angle α, β, γ (deg.)90.000, 90.596, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-401-

CL

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Components

#1: Protein Cembrene A synthase


Mass: 45760.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eleutherobia rubra (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 28% (w/V) PEG 3350, 0.28 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.58→37.97 Å / Num. obs: 52295 / % possible obs: 96.1 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.34 Å2 / Rsym value: 0.046 / Net I/σ(I): 14.7
Reflection shellResolution: 1.58→1.67 Å / Num. unique obs: 8256 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→37.97 Å / SU ML: 0.1843 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.6614
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.192 2619 5.01 %
Rwork0.1615 49665 -
obs0.1631 52284 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.35 Å2
Refinement stepCycle: LAST / Resolution: 1.58→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3099 0 13 187 3299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00513239
X-RAY DIFFRACTIONf_angle_d0.70854384
X-RAY DIFFRACTIONf_chiral_restr0.0437490
X-RAY DIFFRACTIONf_plane_restr0.0039546
X-RAY DIFFRACTIONf_dihedral_angle_d21.27461206
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.58-1.610.27021370.23842445X-RAY DIFFRACTION90.5
1.61-1.640.26391310.19992603X-RAY DIFFRACTION95.83
1.64-1.670.25061370.17582604X-RAY DIFFRACTION95.91
1.67-1.710.20731380.16072612X-RAY DIFFRACTION95.85
1.71-1.750.20311340.14922622X-RAY DIFFRACTION96.43
1.75-1.790.2191390.14482593X-RAY DIFFRACTION95.86
1.79-1.840.21431400.14062525X-RAY DIFFRACTION93.08
1.84-1.890.21061340.14522633X-RAY DIFFRACTION97.19
1.89-1.950.18981420.1562637X-RAY DIFFRACTION96.93
1.95-2.020.19141370.14762629X-RAY DIFFRACTION97.19
2.02-2.110.21651410.14552616X-RAY DIFFRACTION96.57
2.11-2.20.17931340.15062554X-RAY DIFFRACTION93.46
2.2-2.320.18751370.15012668X-RAY DIFFRACTION97.87
2.32-2.460.18661380.15132650X-RAY DIFFRACTION97.31
2.46-2.650.20011390.15542650X-RAY DIFFRACTION97.89
2.65-2.920.21031410.1732590X-RAY DIFFRACTION95.29
2.92-3.340.18911370.18232708X-RAY DIFFRACTION98.61
3.34-4.210.17921400.16052614X-RAY DIFFRACTION95.92
4.21-37.970.17421430.16172712X-RAY DIFFRACTION97.71

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