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- PDB-6loi: Crystal structure of Enterococcus faecalis Undecaprenyl pyrophosp... -

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Basic information

Entry
Database: PDB / ID: 6loi
TitleCrystal structure of Enterococcus faecalis Undecaprenyl pyrophosphate synthase(EfaUPPS)
ComponentsIsoprenyl transferase
KeywordsTRANSFERASE / Isoprenyl transferase
Function / homology
Function and homology information


: / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity / polyprenol biosynthetic process / Transferases; Transferring alkyl or aryl groups, other than methyl groups / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
Di-trans-poly-cis-decaprenylcistransferase-like, conserved site / Undecaprenyl pyrophosphate synthase family signature. / Undecaprenyl pyrophosphate synthetase / Decaprenyl diphosphate synthase-like / Decaprenyl diphosphate synthase-like / Putative undecaprenyl diphosphate synthase / Decaprenyl diphosphate synthase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isoprenyl transferase / Isoprenyl transferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsLin, W. / Wang, C.Y. / Li, W.J. / Wang, F.L.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: Investigations into the Antibacterial Mechanism of Action of Viridicatumtoxins.
Authors: Li, W. / Li, L. / Zhang, C. / Cai, Y. / Gao, Q. / Wang, F. / Cao, Y. / Lin, J. / Li, J. / Shang, Z. / Lin, W.
History
DepositionJan 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.2Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 29, 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: Isoprenyl transferase
B: Isoprenyl transferase
C: Isoprenyl transferase
D: Isoprenyl transferase
E: Isoprenyl transferase
F: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)200,0686
Polymers200,0686
Non-polymers00
Water3,045169
1
A: Isoprenyl transferase

D: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)66,6892
Polymers66,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+y+1,-x,z-1/31
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area19790 Å2
MethodPISA
2
B: Isoprenyl transferase
C: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)66,6892
Polymers66,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-21 kcal/mol
Surface area20750 Å2
MethodPISA
3
E: Isoprenyl transferase
F: Isoprenyl transferase


Theoretical massNumber of molelcules
Total (without water)66,6892
Polymers66,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-22 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.779, 82.779, 213.706
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Isoprenyl transferase


Mass: 33344.656 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria)
Gene: CYQ15_14590, CYQ44_13430, DAI13_12250, EU507_05085, FKY84_09185
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A246M745, UniProt: Q831K9*PLUS, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate acid/sodium hydroxide (pH 5.0), 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 54407 / % possible obs: 96.5 % / Redundancy: 6.6 % / CC1/2: 0.993 / Net I/σ(I): 1.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1926 / CC1/2: 0.778 / CC star: 0.935 / Rpim(I) all: 0.269 / Rrim(I) all: 0.539 / Rsym value: 0.481 / Χ2: 0.786 / % possible all: 69

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UEH

1ueh


Resolution: 2.503→35.351 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 2043 4.42 %
Rwork0.1776 44213 -
obs0.1803 46256 82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.28 Å2 / Biso mean: 46.5375 Å2 / Biso min: 4.27 Å2
Refinement stepCycle: final / Resolution: 2.503→35.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10729 0 0 169 10898
Biso mean---39.01 -
Num. residues----1341
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5032-2.56140.3238510.2313100829
2.5614-2.62540.3412660.2275125635
2.6254-2.69640.3261870.2289152242
2.6964-2.77570.2632950.2358192153
2.7757-2.86530.3171180.2347265474
2.8653-2.96760.27631610.2399351498
2.9676-3.08640.34831650.22633604100
3.0864-3.22670.27281600.19823585100
3.2267-3.39670.25521580.18643591100
3.3967-3.60940.21541600.17063641100
3.6094-3.88770.22471640.16153587100
3.8877-4.27840.20971580.14623585100
4.2784-4.89610.19551720.14133605100
4.8961-6.16320.22761680.17753575100
6.1632-35.3510.19851600.159356599

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