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- PDB-3v4x: The Biochemical and Structural Basis for Inhibition of Enterococc... -

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Basic information

Entry
Database: PDB / ID: 3v4x
TitleThe Biochemical and Structural Basis for Inhibition of Enterococcus faecalis HMG-CoA Synthase, mvaS, by Hymeglusin
ComponentsHMG-CoA synthase
KeywordsTransferase/Inhibitor / HYDROXYMETHYLGLUTARYL-CoA SYNTHASE / Hymeglusin covalent adduct / Transferase-Inhibitor complex
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA synthase / hydroxymethylglutaryl-CoA synthase activity / acetyl-CoA metabolic process / isoprenoid 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
Chem-F24 / Hydroxymethylglutaryl-CoA synthase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.952 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 1.1Nov 27, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)171,6938
Polymers170,3884
Non-polymers1,3064
Water19,5821087
1
A: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9232
Polymers42,5971
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9232
Polymers42,5971
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9232
Polymers42,5971
Non-polymers3261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9232
Polymers42,5971
Non-polymers3261
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)85,8474
Polymers85,1942
Non-polymers6532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-15 kcal/mol
Surface area25280 Å2
MethodPISA
6
C: HMG-CoA synthase
hetero molecules

D: HMG-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8474
Polymers85,1942
Non-polymers6532
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y+1/2,-z-11
Buried area7370 Å2
ΔGint-19 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.333, 52.756, 117.576
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HMG-CoA synthase


Mass: 42596.934 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-F24 / (7R,12R,13R)-13-formyl-12,14-dihydroxy-3,5,7-trimethyltetradeca-2,4-dienoic acid / Antibiotic 1233A, Bound Form


Mass: 326.428 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H30O5 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1087 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 298 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 298K

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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: 1.95→48.02 Å / Num. all: 96022 / Num. obs: 92978 / % possible obs: 96.8 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.8 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 11.27

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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
Starting model: PDB ENTRY 1X9E

1x9e


Resolution: 1.952→48.02 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2182 9271 9.99 %
Rwork0.1707 --
obs0.1755 92792 96.82 %
all-96022 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.37 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.1838 Å20 Å2-3.0147 Å2
2---2.8171 Å20 Å2
3----0.3667 Å2
Refinement stepCycle: LAST / Resolution: 1.952→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11954 0 92 1087 13133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112270
X-RAY DIFFRACTIONf_angle_d1.24916636
X-RAY DIFFRACTIONf_dihedral_angle_d13.6194482
X-RAY DIFFRACTIONf_chiral_restr0.1141893
X-RAY DIFFRACTIONf_plane_restr0.0032153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.952-1.97440.30232380.24012055X-RAY DIFFRACTION73
1.9744-1.99770.24482940.21032573X-RAY DIFFRACTION91
1.9977-2.0220.25252940.20312703X-RAY DIFFRACTION94
2.022-2.04760.27532820.20182766X-RAY DIFFRACTION95
2.0476-2.07460.26273170.19032674X-RAY DIFFRACTION96
2.0746-2.1030.26663120.19192766X-RAY DIFFRACTION96
2.103-2.1330.24182950.18412716X-RAY DIFFRACTION96
2.133-2.16490.2373180.18052731X-RAY DIFFRACTION96
2.1649-2.19870.24193000.17882798X-RAY DIFFRACTION96
2.1987-2.23480.21893210.17062721X-RAY DIFFRACTION97
2.2348-2.27330.23482830.17572808X-RAY DIFFRACTION97
2.2733-2.31460.25233020.1772788X-RAY DIFFRACTION97
2.3146-2.35910.23613130.16592768X-RAY DIFFRACTION97
2.3591-2.40730.22323310.16362767X-RAY DIFFRACTION97
2.4073-2.45960.23082880.1712765X-RAY DIFFRACTION97
2.4596-2.51690.23063040.17142846X-RAY DIFFRACTION98
2.5169-2.57980.22013090.16762773X-RAY DIFFRACTION98
2.5798-2.64950.24553210.17452804X-RAY DIFFRACTION98
2.6495-2.72750.22193160.17312832X-RAY DIFFRACTION99
2.7275-2.81550.22832970.17392860X-RAY DIFFRACTION99
2.8155-2.91610.21383240.16922860X-RAY DIFFRACTION99
2.9161-3.03290.21433270.16672834X-RAY DIFFRACTION100
3.0329-3.17090.22013240.1792902X-RAY DIFFRACTION100
3.1709-3.3380.22043100.17662874X-RAY DIFFRACTION100
3.338-3.54710.21213150.16972896X-RAY DIFFRACTION100
3.5471-3.82090.20833310.14932874X-RAY DIFFRACTION100
3.8209-4.20520.16453260.13192898X-RAY DIFFRACTION100
4.2052-4.81320.14713210.1242941X-RAY DIFFRACTION100
4.8132-6.06220.18523220.14842930X-RAY DIFFRACTION100
6.0622-48.03440.26793360.23932998X-RAY DIFFRACTION99

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