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- PDB-3v4n: The Biochemical and Structural Basis for Inhibition of Enterococc... -

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Basic information

Entry
Database: PDB / ID: 3v4n
TitleThe Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthatse, mvaS, by Hymeglusin
ComponentsHMG-CoA synthase
KeywordsTransferase/Inhibitor / HYDROXYMETHYLGLUTARYL-CoA SYNTHASE / NITROSYLATION / Transferase-Inhibitor complex
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / farnesyl diphosphate biosynthetic process, mevalonate pathway / acetyl-CoA metabolic process / ergosterol biosynthetic process
Similarity search - Function
Hydroxymethylglutaryl-CoA synthase, prokaryotic / Hydroxymethylglutaryl-coenzyme A synthase, N-terminal / Hydroxymethylglutaryl-coenzyme A synthase, C-terminal domain / Hydroxymethylglutaryl-coenzyme A synthase N terminal / Hydroxymethylglutaryl-coenzyme A synthase C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSkaff, D.A. / Ramyar, K.X. / McWhorter, W.J. / Geisbrecht, B.V. / Miziorko, H.M.
CitationJournal: Biochemistry / Year: 2012
Title: Biochemical and structural basis for inhibition of Enterococcus faecalis hydroxymethylglutaryl-CoA synthase, mvaS, by hymeglusin.
Authors: Skaff, D.A. / Ramyar, K.X. / McWhorter, W.J. / Barta, M.L. / Geisbrecht, B.V. / Miziorko, H.M.
History
DepositionDec 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Sep 10, 2014Group: Refinement description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HMG-CoA synthase
B: HMG-CoA synthase
C: HMG-CoA synthase
D: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7135
Polymers170,5044
Non-polymers2091
Water26,9141494
1
A: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)42,6261
Polymers42,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8352
Polymers42,6261
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)42,6261
Polymers42,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)42,6261
Polymers42,6261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: HMG-CoA synthase
B: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4613
Polymers85,2522
Non-polymers2091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-16 kcal/mol
Surface area26180 Å2
MethodPISA
6
C: HMG-CoA synthase

D: HMG-CoA synthase


Theoretical massNumber of molelcules
Total (without water)85,2522
Polymers85,2522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area5630 Å2
ΔGint-17 kcal/mol
Surface area25470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.531, 56.279, 123.893
Angle α, β, γ (deg.)90.00, 100.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HMG-CoA synthase


Mass: 42625.930 Da / Num. of mol.: 4 / Mutation: A163S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: ATCC 4200 / Gene: mvaS / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9FD71, hydroxymethylglutaryl-CoA synthase
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1494 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 23% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2011
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40.24 Å / Num. all: 197160 / Num. obs: 193837 / % possible obs: 98.3 % / Observed criterion σ(F): 3.5 / Observed criterion σ(I): 3.5 / Redundancy: 6.7 % / Biso Wilson estimate: 17.12 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.25

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→26.965 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 20.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 18667 10 %RANDOM
Rwork0.1411 ---
obs0.1464 193837 98.32 %-
all-197160 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6759 Å20 Å2-0.5297 Å2
2--5.4355 Å2-0 Å2
3----2.7596 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11917 0 14 1494 13425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312230
X-RAY DIFFRACTIONf_angle_d0.72416610
X-RAY DIFFRACTIONf_dihedral_angle_d13.6794495
X-RAY DIFFRACTIONf_chiral_restr0.0441891
X-RAY DIFFRACTIONf_plane_restr0.0022156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61590.30755930.21195342X-RAY DIFFRACTION91
1.6159-1.63490.28196310.19375676X-RAY DIFFRACTION96
1.6349-1.65490.27186210.17825589X-RAY DIFFRACTION95
1.6549-1.67580.25666410.16215753X-RAY DIFFRACTION98
1.6758-1.69790.22946250.1595625X-RAY DIFFRACTION96
1.6979-1.72110.23826380.14635747X-RAY DIFFRACTION98
1.7211-1.74570.21796410.1485774X-RAY DIFFRACTION98
1.7457-1.77180.23736310.14815676X-RAY DIFFRACTION97
1.7718-1.79940.22076400.13615768X-RAY DIFFRACTION98
1.7994-1.82890.21766410.13565766X-RAY DIFFRACTION98
1.8289-1.86050.21486440.13315806X-RAY DIFFRACTION99
1.8605-1.89430.21576430.13265777X-RAY DIFFRACTION98
1.8943-1.93070.19656440.12725793X-RAY DIFFRACTION99
1.9307-1.97010.20736460.13255832X-RAY DIFFRACTION99
1.9701-2.01290.20166460.13565810X-RAY DIFFRACTION98
2.0129-2.05970.20836520.1335873X-RAY DIFFRACTION100
2.0597-2.11120.19436470.1345814X-RAY DIFFRACTION99
2.1112-2.16830.19766490.13615847X-RAY DIFFRACTION99
2.1683-2.23210.19586570.12975912X-RAY DIFFRACTION100
2.2321-2.30410.20226470.13385826X-RAY DIFFRACTION99
2.3041-2.38640.19556560.13025898X-RAY DIFFRACTION99
2.3864-2.48190.20036520.13395873X-RAY DIFFRACTION100
2.4819-2.59470.19346570.13795899X-RAY DIFFRACTION100
2.5947-2.73140.21266560.15455911X-RAY DIFFRACTION100
2.7314-2.90230.20936610.14895950X-RAY DIFFRACTION100
2.9023-3.12610.19066610.14675947X-RAY DIFFRACTION100
3.1261-3.44020.19766590.15275933X-RAY DIFFRACTION100
3.4402-3.93660.18096640.13925977X-RAY DIFFRACTION100
3.9366-4.95470.13826690.11916019X-RAY DIFFRACTION100
4.9547-26.9650.16846710.15416041X-RAY DIFFRACTION98

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