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- PDB-7vwt: Carbazole Prenyl Transferase CqsB4 -

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Basic information

Entry
Database: PDB / ID: 7vwt
TitleCarbazole Prenyl Transferase CqsB4
ComponentsCqsB4
KeywordsTRANSFERASE / Prenyl transferase / Squalene synthase
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha / Chem-AO6 / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSuemune, H. / Nagata, R. / Kuzuyama, T. / Nagano, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H04658 Japan
Japan Society for the Promotion of Science (JSPS)19H05780 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Structural Basis for the Prenylation Reaction of Carbazole-Containing Natural Products Catalyzed by Squalene Synthase-Like Enzymes.
Authors: Nagata, R. / Suemune, H. / Kobayashi, M. / Shinada, T. / Shin-Ya, K. / Nishiyama, M. / Hino, T. / Sato, Y. / Kuzuyama, T. / Nagano, S.
History
DepositionNov 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CqsB4
B: CqsB4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0649
Polymers77,0392
Non-polymers1,0257
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-51 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.261, 85.251, 113.405
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CqsB4


Mass: 38519.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 281 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AO6 / 2-methyl-1-[(2R)-2-oxidanylpropyl]-9H-carbazole-3,4-dione


Mass: 269.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / Details: LiSO4, PEG 3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 0.999999 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 1.73→44.84 Å / Num. obs: 74583 / % possible obs: 99.76 % / Redundancy: 2 % / Biso Wilson estimate: 31.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.43
Reflection shellResolution: 1.73→1.792 Å / Num. unique obs: 14623 / CC1/2: 0.603

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alpha Fold2 model

Resolution: 1.73→44.84 Å / SU ML: 0.3622 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.6342
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2354 3824 5.1 %
Rwork0.1978 71187 -
obs0.1998 74583 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 1.73→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5246 0 68 274 5588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01035438
X-RAY DIFFRACTIONf_angle_d1.02717375
X-RAY DIFFRACTIONf_chiral_restr0.0515790
X-RAY DIFFRACTIONf_plane_restr0.007953
X-RAY DIFFRACTIONf_dihedral_angle_d23.261999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.750.52211300.50022581X-RAY DIFFRACTION98.08
1.75-1.770.5311400.48412578X-RAY DIFFRACTION99.31
1.77-1.80.55671370.47082614X-RAY DIFFRACTION99.6
1.8-1.820.44241320.45132586X-RAY DIFFRACTION99.52
1.82-1.850.44131410.39932610X-RAY DIFFRACTION99.49
1.85-1.880.36131260.35772627X-RAY DIFFRACTION99.57
1.88-1.910.32281290.32182598X-RAY DIFFRACTION99.56
1.91-1.940.33021320.30082628X-RAY DIFFRACTION99.64
1.94-1.980.30891310.27352612X-RAY DIFFRACTION99.71
1.98-2.010.30031300.2612615X-RAY DIFFRACTION99.67
2.01-2.060.30981520.23832592X-RAY DIFFRACTION99.71
2.06-2.10.29051540.2132609X-RAY DIFFRACTION99.64
2.1-2.150.24731290.20192628X-RAY DIFFRACTION99.78
2.15-2.20.22261590.18972610X-RAY DIFFRACTION99.96
2.2-2.260.22341710.17712593X-RAY DIFFRACTION99.96
2.26-2.330.25051690.17142585X-RAY DIFFRACTION99.89
2.33-2.40.23311480.17932645X-RAY DIFFRACTION99.93
2.4-2.490.22531450.18122627X-RAY DIFFRACTION99.93
2.49-2.590.25771350.18992655X-RAY DIFFRACTION100
2.59-2.710.23191280.18712650X-RAY DIFFRACTION99.93
2.71-2.850.26011340.19592676X-RAY DIFFRACTION99.96
2.85-3.030.2421380.19312646X-RAY DIFFRACTION100
3.03-3.260.23451520.19722663X-RAY DIFFRACTION99.96
3.26-3.590.21311320.18652682X-RAY DIFFRACTION100
3.59-4.110.1791450.16032700X-RAY DIFFRACTION99.96
4.11-5.180.19731420.15092737X-RAY DIFFRACTION99.93
5.18-44.840.21630.17792840X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -17.561 Å / Origin y: 21.82 Å / Origin z: -21.719 Å
111213212223313233
T0.187952636123 Å20.0221362700422 Å20.015801568319 Å2-0.239717245426 Å2-0.0500980692192 Å2--0.235791458299 Å2
L0.690363218683 °20.0607548100168 °20.130724003431 °2-0.444075513952 °2-0.202214318783 °2--0.281321846065 °2
S-0.0044918257745 Å °-0.0105698861031 Å °0.0845500940961 Å °-0.0100628704262 Å °0.0190738703945 Å °0.0516367788836 Å °0.00888695711601 Å °-0.00586197474293 Å °-0.01326414673 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )A-1 - 327
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )A701 - 703
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )A801 - 962
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )A704 - 705
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )B0 - 327
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )B401
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )B501 - 612
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID -1:327 OR RESID 701:703 OR RESID 801:962 OR RESID 704:705 ) ) OR ( CHAIN B AND ( RESID 0:327 OR RESID 401:401 OR RESID 501:612 OR RESID 402:402 ) )B402

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