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- PDB-5xk3: Crystal structure of apo form Isosesquilavandulyl Diphosphate Syn... -

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Basic information

Entry
Database: PDB / ID: 5xk3
TitleCrystal structure of apo form Isosesquilavandulyl Diphosphate Synthase from Streptomyces sp. strain CNH-189
ComponentsUndecaprenyl diphosphate synthase
KeywordsTRANSFERASE / prenyltransferase / antibiotic biosynthesis
Function / homologyDecaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / transferase activity, transferring alkyl or aryl (other than methyl) groups / Undecaprenyl diphosphate synthase
Function and homology information
Biological speciesStreptomyces sp. CNH189 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.996 Å
AuthorsKo, T.P. / Guo, R.T. / Liu, W. / Chen, C.C. / Gao, J.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: "Head-to-Middle" and "Head-to-Tail" cis-Prenyl Transferases: Structure of Isosesquilavandulyl Diphosphate Synthase.
Authors: Gao, J. / Ko, T.P. / Chen, L. / Malwal, S.R. / Zhang, J. / Hu, X. / Qu, F. / Liu, W. / Huang, J.W. / Cheng, Y.S. / Chen, C.C. / Yang, Y. / Zhang, Y. / Oldfield, E. / Guo, R.T.
History
DepositionMay 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,40910
Polymers106,8334
Non-polymers5766
Water16,592921
1
A: Undecaprenyl diphosphate synthase
B: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7055
Polymers53,4162
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-80 kcal/mol
Surface area17600 Å2
MethodPISA
2
C: Undecaprenyl diphosphate synthase
D: Undecaprenyl diphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7055
Polymers53,4162
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-79 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.115, 121.198, 126.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Undecaprenyl diphosphate synthase


Mass: 26708.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CNH189 (bacteria) / Gene: mcl22 / Plasmid: pET46Ek/LIC
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: M4T4U9
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 921 / Source method: isolated from a natural source / Formula: H2O

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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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: PROTEIN: 10 mg/mL in 25 mM Tris-Cl (pH 7.5), 150 mM NaCl RESERVOIR: 0.2 M (NH4)2SO4, 0.1 M MES pH 6.5, 30% PEG 5000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 30, 2016
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.996→25 Å / Num. obs: 71134 / % possible obs: 99.2 % / Redundancy: 4.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.8
Reflection shellResolution: 1.996→2.07 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6984 / CC1/2: 0.947 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VFW

2vfw


Resolution: 1.996→24.278 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.89
RfactorNum. reflection% reflectionSelection details
Rfree0.1999 2001 2.82 %random
Rwork0.1688 ---
obs0.1697 71081 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.996→24.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6842 0 30 921 7793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067028
X-RAY DIFFRACTIONf_angle_d0.8259530
X-RAY DIFFRACTIONf_dihedral_angle_d20.1734186
X-RAY DIFFRACTIONf_chiral_restr0.051041
X-RAY DIFFRACTIONf_plane_restr0.0051231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9959-2.04580.28041280.23794628X-RAY DIFFRACTION94
2.0458-2.10110.26551370.22414865X-RAY DIFFRACTION99
2.1011-2.16290.23511500.20194894X-RAY DIFFRACTION99
2.1629-2.23270.26011320.1884908X-RAY DIFFRACTION100
2.2327-2.31240.20441560.18284926X-RAY DIFFRACTION99
2.3124-2.40490.21171370.17374921X-RAY DIFFRACTION100
2.4049-2.51430.20831450.1744938X-RAY DIFFRACTION100
2.5143-2.64670.2121440.17834960X-RAY DIFFRACTION100
2.6467-2.81230.23871440.18074963X-RAY DIFFRACTION100
2.8123-3.0290.19111440.18234983X-RAY DIFFRACTION100
3.029-3.33320.21541470.17684985X-RAY DIFFRACTION100
3.3332-3.81390.19371450.15865029X-RAY DIFFRACTION100
3.8139-4.7990.16791450.14075018X-RAY DIFFRACTION99
4.799-24.27940.1751470.15825062X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 7.9629 Å / Origin y: 74.0296 Å / Origin z: 44.2587 Å
111213212223313233
T0.2399 Å2-0.0205 Å20.0344 Å2-0.2531 Å2-0.021 Å2--0.2526 Å2
L0.2108 °2-0.1343 °20.1097 °2-0.5404 °2-0.2411 °2--0.6449 °2
S0.0312 Å °-0.0572 Å °0.0189 Å °-0.04 Å °-0.0236 Å °0.0356 Å °0.0656 Å °0.0575 Å °-0 Å °
Refinement TLS groupSelection details: all

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