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- PDB-8b4l: Crystal structure of a selenomethionine-labeled hydropyrene synth... -

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Basic information

Entry
Database: PDB / ID: 8b4l
TitleCrystal structure of a selenomethionine-labeled hydropyrene synthase (M75L variant) in its closed conformation
ComponentsTerpene synthase
KeywordsLYASE / Diterpene Synthase / Pseudopterosins / GGDP / Hydropyrene Synthase
Function / homology
Function and homology information


hydropyrene synthase / hydropyrenol synthase / isoelisabethatriene synthase / terpene synthase activity / metal ion binding
Similarity search - Function
Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / Hydropyrene synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.394 Å
AuthorsHelmer, C.P.O. / Driller, R. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German-Israeli Foundation for Research and DevelopmentI-85-302.14-2018 Germany
CitationJournal: To Be Published
Title: crystal structure of s hydropyrene synthase in its closed conformation
Authors: Helmer, C.P.O. / Driller, R. / Loll, B.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Terpene synthase
A: Terpene synthase
B: Terpene synthase
C: Terpene synthase
D: Terpene synthase
F: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,65228
Polymers218,7936
Non-polymers1,85922
Water00
1
E: Terpene synthase
A: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,56710
Polymers72,9312
Non-polymers6368
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-70 kcal/mol
Surface area24560 Å2
MethodPISA
2
B: Terpene synthase
D: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,56710
Polymers72,9312
Non-polymers6368
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-72 kcal/mol
Surface area24440 Å2
MethodPISA
3
C: Terpene synthase
hetero molecules

F: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5188
Polymers72,9312
Non-polymers5876
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area4340 Å2
ΔGint-53 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.698, 176.688, 185.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 89 or resid 94...
21(chain B and (resid 3 through 89 or resid 94...
31(chain C and (resid 3 through 89 or resid 94...
41(chain D and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))
51(chain E and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))
61(chain F and (resid 3 through 89 or resid 94...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILETHRTHR(chain A and (resid 3 through 89 or resid 94...AB3 - 895 - 91
12GLYGLYTYRTYR(chain A and (resid 3 through 89 or resid 94...AB94 - 15396 - 155
13GLUGLUSERSER(chain A and (resid 3 through 89 or resid 94...AB155 - 308157 - 310
14MGMGAHDAHD(chain A and (resid 3 through 89 or resid 94...AM - N403 - 404
21ILEILETHRTHR(chain B and (resid 3 through 89 or resid 94...BC3 - 895 - 91
22GLYGLYTYRTYR(chain B and (resid 3 through 89 or resid 94...BC94 - 15396 - 155
23GLUGLUSERSER(chain B and (resid 3 through 89 or resid 94...BC155 - 308157 - 310
24MGMGAHDAHD(chain B and (resid 3 through 89 or resid 94...BQ - R403 - 404
31ILEILETHRTHR(chain C and (resid 3 through 89 or resid 94...CD3 - 895 - 91
32GLYGLYTYRTYR(chain C and (resid 3 through 89 or resid 94...CD94 - 15396 - 155
33GLUGLUSERSER(chain C and (resid 3 through 89 or resid 94...CD155 - 308157 - 310
34MGMGAHDAHD(chain C and (resid 3 through 89 or resid 94...CU - V403 - 404
41ILEILETYRTYR(chain D and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))DE3 - 1535 - 155
42GLUGLUSERSER(chain D and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))DE155 - 308157 - 310
43MGMGAHDAHD(chain D and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))DY - Z403 - 404
51ILEILETYRTYR(chain E and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))EA3 - 1535 - 155
52GLUGLUSERSER(chain E and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))EA155 - 308157 - 310
53MGMGAHDAHD(chain E and (resid 3 through 153 or resid 155 through 308 or resid 403 through 404))EI - J403 - 404
61ILEILETHRTHR(chain F and (resid 3 through 89 or resid 94...FF3 - 895 - 91
62GLYGLYTYRTYR(chain F and (resid 3 through 89 or resid 94...FF94 - 15396 - 155
63GLUGLUSERSER(chain F and (resid 3 through 89 or resid 94...FF155 - 308157 - 310
64MGMGAHDAHD(chain F and (resid 3 through 89 or resid 94...FAA - BA401 - 402

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Components

#1: Protein
Terpene synthase


Mass: 36465.453 Da / Num. of mol.: 6 / Mutation: M75L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p0765 / Plasmid: pTRX / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D5SK09, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AHD / 4-AMINO-1-HYDROXYBUTANE-1,1-DIYLDIPHOSPHONATE / ALENDRONATE / FOSAMAX (TM)


Mass: 245.064 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H9NO7P2 / Comment: medication*YM
Has ligand of interestN
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/NaOH pH 7.5, 21% PEG 10000 (w/v) and 1% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 3.39→50 Å / Num. obs: 70442 / % possible obs: 99.3 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rrim(I) all: 0.321 / Net I/σ(I): 9.4
Reflection shellResolution: 3.39→3.6 Å / Num. unique obs: 70442 / CC1/2: 0.62 / Rrim(I) all: 2.849

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.394→49.107 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 34.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 2099 2.99 %
Rwork0.2375 68139 -
obs0.2387 70238 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 277.41 Å2 / Biso mean: 107.158 Å2 / Biso min: 52.03 Å2
Refinement stepCycle: final / Resolution: 3.394→49.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14538 0 100 0 14638
Biso mean--136 --
Num. residues----1843
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5292X-RAY DIFFRACTION2.757TORSIONAL
12B5292X-RAY DIFFRACTION2.757TORSIONAL
13C5292X-RAY DIFFRACTION2.757TORSIONAL
14D5292X-RAY DIFFRACTION2.757TORSIONAL
15E5292X-RAY DIFFRACTION2.757TORSIONAL
16F5292X-RAY DIFFRACTION2.757TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3941-3.4730.43191290.4048414991
3.473-3.55990.43471390.3854591100
3.5599-3.65610.44191410.33184575100
3.6561-3.76360.38631390.31464538100
3.7636-3.88510.37211440.30134652100
3.8851-4.02390.29921390.27474539100
4.0239-4.18490.30141420.24944532100
4.1849-4.37520.31051370.23944537100
4.3752-4.60570.23081430.21024593100
4.6057-4.89410.24151450.20134601100
4.8941-5.27150.28021420.22484562100
5.2715-5.80130.27031450.2134579100
5.8013-6.6390.23761430.214580100
6.639-8.35770.21751360.19174576100
8.3577-49.1070.19621350.2009453599

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