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- PDB-8b4m: Crystal structure of a hydropyrene synthase (M75L variant) in its... -

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Basic information

Entry
Database: PDB / ID: 8b4m
TitleCrystal structure of a hydropyrene synthase (M75L variant) in its closed conformation
ComponentsTerpene synthase
KeywordsLYASE / Diterpene Synthase / Pseudopterosins / GGDP / Hydropyrene Synthase
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / Terpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / ALENDRONATE / Terpene synthase
Function and homology information
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)217,12222
Polymers215,8346
Non-polymers1,28816
Water0
1
A: Terpene synthase
B: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2676
Polymers71,9452
Non-polymers3224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-36 kcal/mol
Surface area26300 Å2
MethodPISA
2
D: Terpene synthase
hetero molecules

C: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)72,2676
Polymers71,9452
Non-polymers3224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area3680 Å2
ΔGint-37 kcal/mol
Surface area25880 Å2
MethodPISA
3
E: Terpene synthase
hetero molecules

F: Terpene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,58910
Polymers71,9452
Non-polymers6448
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area4610 Å2
ΔGint-66 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.722, 82.316, 148.294
Angle α, β, γ (deg.)90.000, 92.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 37 or resid 43...
21(chain B and (resid 2 through 37 or resid 43...
31(chain C and (resid 2 through 37 or resid 43...
41(chain D and (resid 2 through 37 or resid 43 through 153 or resid 155 through 307))
51(chain E and (resid 2 through 37 or resid 43...
61(chain F and (resid 2 through 37 or resid 43...

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
11THRTHRMETMET(chain A and (resid 2 through 37 or resid 43...AA2 - 373 - 38
12ALAALAASPASP(chain A and (resid 2 through 37 or resid 43...AA43 - 8744 - 88
13LEULEUTYRTYR(chain A and (resid 2 through 37 or resid 43...AA95 - 15396 - 154
14GLUGLUTRPTRP(chain A and (resid 2 through 37 or resid 43...AA155 - 307156 - 308
21THRTHRMETMET(chain B and (resid 2 through 37 or resid 43...BB2 - 373 - 38
22ALAALAASPASP(chain B and (resid 2 through 37 or resid 43...BB43 - 8744 - 88
23LEULEUTYRTYR(chain B and (resid 2 through 37 or resid 43...BB95 - 15396 - 154
24GLUGLUTRPTRP(chain B and (resid 2 through 37 or resid 43...BB155 - 307156 - 308
31THRTHRMETMET(chain C and (resid 2 through 37 or resid 43...CC2 - 373 - 38
32ALAALAASPASP(chain C and (resid 2 through 37 or resid 43...CC43 - 8744 - 88
33LEULEUTYRTYR(chain C and (resid 2 through 37 or resid 43...CC95 - 15396 - 154
34GLUGLUTRPTRP(chain C and (resid 2 through 37 or resid 43...CC155 - 307156 - 308
41THRTHRMETMET(chain D and (resid 2 through 37 or resid 43 through 153 or resid 155 through 307))DD2 - 373 - 38
42ALAALATYRTYR(chain D and (resid 2 through 37 or resid 43 through 153 or resid 155 through 307))DD43 - 15344 - 154
43GLUGLUTRPTRP(chain D and (resid 2 through 37 or resid 43 through 153 or resid 155 through 307))DD155 - 307156 - 308
51THRTHRMETMET(chain E and (resid 2 through 37 or resid 43...EE2 - 373 - 38
52ALAALAASPASP(chain E and (resid 2 through 37 or resid 43...EE43 - 8744 - 88
53LEULEUTYRTYR(chain E and (resid 2 through 37 or resid 43...EE95 - 15396 - 154
54GLUGLUTRPTRP(chain E and (resid 2 through 37 or resid 43...EE155 - 307156 - 308
61THRTHRMETMET(chain F and (resid 2 through 37 or resid 43...FF2 - 373 - 38
62ALAALAASPASP(chain F and (resid 2 through 37 or resid 43...FF43 - 8744 - 88
63LEULEUTYRTYR(chain F and (resid 2 through 37 or resid 43...FF95 - 15396 - 154
64GLUGLUTRPTRP(chain F and (resid 2 through 37 or resid 43...FF155 - 307156 - 308

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Components

#1: Protein
Terpene synthase /


Mass: 35972.324 Da / Num. of mol.: 6 / Mutation: M75L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Gene: SCLAV_p0765
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D5SK09, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-212 / ALENDRONATE / (4-AMINO-1-HYDROXY-1-PHOSPHONO-BUTYL)PHOSPHONIC ACID / Alendronic acid


Mass: 249.096 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H13NO7P2 / Comment: medication*YM
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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Naformiat and 19% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9841 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 3.04→50 Å / Num. obs: 48303 / % possible obs: 96.9 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rrim(I) all: 0.31 / Net I/σ(I): 5.1
Reflection shellResolution: 3.04→3.15 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 7398 / CC1/2: 0.439 / Rrim(I) all: 1.524

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: XXXX

Resolution: 3.04→49.538 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3074 2097 4.35 %
Rwork0.2521 46137 -
obs0.2545 48234 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.63 Å2 / Biso mean: 58.5177 Å2 / Biso min: 15.77 Å2
Refinement stepCycle: final / Resolution: 3.04→49.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14554 0 68 0 14622
Biso mean--78.51 --
Num. residues----1841
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5370X-RAY DIFFRACTION10.502TORSIONAL
12B5370X-RAY DIFFRACTION10.502TORSIONAL
13C5370X-RAY DIFFRACTION10.502TORSIONAL
14D5370X-RAY DIFFRACTION10.502TORSIONAL
15E5370X-RAY DIFFRACTION10.502TORSIONAL
16F5370X-RAY DIFFRACTION10.502TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.04-3.11040.42641240.3554272187
3.1104-3.18820.35751390.3287306197
3.1882-3.27440.38931400.328307097
3.2744-3.37070.37811380.3062304297
3.3707-3.47950.37151380.3075303097
3.4795-3.60380.33471390.3034306396
3.6038-3.7480.38771410.2929309497
3.748-3.91860.34991410.2744310999
3.9186-4.12510.31021400.2693307897
4.1251-4.38340.30831380.2311302396
4.3834-4.72160.31231440.21973177100
4.7216-5.19620.26141450.21533190100
5.1962-5.94710.28941440.2283317199
5.9471-7.48850.27781440.2303317299
7.4885-49.530.20141420.1919313695

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