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- PDB-7uli: Apo HMG-CoA Reductase from Arabidopsis thaliana (HMG1) -

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Basic information

Entry
Database: PDB / ID: 7uli
TitleApo HMG-CoA Reductase from Arabidopsis thaliana (HMG1)
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase 1
KeywordsOXIDOREDUCTASE / Apo
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / coenzyme A metabolic process / isoprenoid biosynthetic process / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site ...Hydroxymethylglutaryl-CoA reductase, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / Hydroxymethylglutaryl-coenzyme A reductases signature 3. / Hydroxymethylglutaryl-CoA reductase, class I/II / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain superfamily / Hydroxymethylglutaryl-CoA reductase, class I/II, conserved site / Hydroxymethylglutaryl-coenzyme A reductase / Hydroxymethylglutaryl-coenzyme A reductases family profile.
Similarity search - Domain/homology
3-hydroxy-3-methylglutaryl-coenzyme A reductase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHaywood, J. / Bond, C.S.
Funding support Australia, 3items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE180101445 Australia
Australian Research Council (ARC)DP190101048 Australia
Australian Research Council (ARC)LE190100123 Australia
Citation
Journal: Nat Commun / Year: 2022
Title: A fungal tolerance trait and selective inhibitors proffer HMG-CoA reductase as a herbicide mode-of-action.
Authors: Haywood, J. / Breese, K.J. / Zhang, J. / Waters, M.T. / Bond, C.S. / Stubbs, K.A. / Mylne, J.S.
#1: Journal: Biorxiv / Year: 2022
Title: Structure-guided investigations into HMG-CoA reductase as a herbicide target
Authors: Haywood, J. / Breese, K.J. / Zhang, J. / Waters, M.T. / Bond, C.S. / Stubbs, K.A. / Mylne, J.S.
History
DepositionApr 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Oct 18, 2023Group: 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
AAA: 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1


Theoretical massNumber of molelcules
Total (without water)63,6611
Polymers63,6611
Non-polymers00
Water1,63991
1
AAA: 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1

AAA: 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1

AAA: 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1

AAA: 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1


Theoretical massNumber of molelcules
Total (without water)254,6424
Polymers254,6424
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area21050 Å2
ΔGint-136 kcal/mol
Surface area47690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.578, 85.578, 266.654
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11AAA-679-

HOH

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Components

#1: Protein 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 / AtHMGR1 / HMG-CoA reductase 1


Mass: 63660.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HMG1, HMGR1, At1g76490, F14G6.9, F15M4.1 / Production host: Escherichia coli (E. coli)
References: UniProt: P14891, hydroxymethylglutaryl-CoA reductase (NADPH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.92 Å3/Da / Density % sol: 35.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES, 35% w/v poly(acrylic acid sodium salt)2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.9→45.302 Å / Num. obs: 39592 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 14.8
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2488 / CC1/2: 0.549

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HW8

1hw8


Resolution: 1.9→45.302 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.185 / SU B: 5.331 / SU ML: 0.14 / Average fsc free: 0.8225 / Average fsc work: 0.8248 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.243 2031 5.135 %
Rwork0.2073 37524 -
all0.209 --
obs-39555 99.944 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.286 Å2
Baniso -1Baniso -2Baniso -3
1-1.981 Å20 Å2-0 Å2
2--1.981 Å2-0 Å2
3----3.962 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2657 0 0 92 2749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132693
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172563
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.6253635
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5755880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3715373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96323.084107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.16115429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7441513
X-RAY DIFFRACTIONr_chiral_restr0.0620.2371
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023114
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02580
X-RAY DIFFRACTIONr_nbd_refined0.1840.2471
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.22139
X-RAY DIFFRACTIONr_nbtor_refined0.1460.21335
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21195
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.290
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0910.28
X-RAY DIFFRACTIONr_nbd_other0.1830.277
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.215
X-RAY DIFFRACTIONr_mcbond_it3.2425.0271500
X-RAY DIFFRACTIONr_mcbond_other3.2395.0251499
X-RAY DIFFRACTIONr_mcangle_it4.2727.5041862
X-RAY DIFFRACTIONr_mcangle_other4.2727.5051863
X-RAY DIFFRACTIONr_scbond_it4.0035.2051192
X-RAY DIFFRACTIONr_scbond_other4.0015.2061193
X-RAY DIFFRACTIONr_scangle_it5.3267.6861773
X-RAY DIFFRACTIONr_scangle_other5.3247.6861774
X-RAY DIFFRACTIONr_lrange_it5.79960.1952805
X-RAY DIFFRACTIONr_lrange_other5.78560.1582799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.4851150.4232747X-RAY DIFFRACTION99.8953
1.949-2.0030.3431600.3732641X-RAY DIFFRACTION99.9643
2.003-2.0610.3521280.3312594X-RAY DIFFRACTION100
2.061-2.1240.3241330.3062541X-RAY DIFFRACTION100
2.124-2.1940.2921190.2612439X-RAY DIFFRACTION99.9609
2.194-2.2710.2641350.2532347X-RAY DIFFRACTION100
2.271-2.3570.281280.2282290X-RAY DIFFRACTION99.9587
2.357-2.4530.2721100.2182228X-RAY DIFFRACTION100
2.453-2.5620.2581260.2152105X-RAY DIFFRACTION100
2.562-2.6870.2991090.2012033X-RAY DIFFRACTION99.9533
2.687-2.8320.2251080.1911938X-RAY DIFFRACTION99.9511
2.832-3.0040.22900.1871839X-RAY DIFFRACTION100
3.004-3.2110.2171040.1781727X-RAY DIFFRACTION100
3.211-3.4680.198990.1811605X-RAY DIFFRACTION99.9413
3.468-3.7990.249940.1831495X-RAY DIFFRACTION99.9371
3.799-4.2470.238770.1751360X-RAY DIFFRACTION99.9305
4.247-4.9030.181690.1641216X-RAY DIFFRACTION99.8446
4.903-6.0030.238490.21050X-RAY DIFFRACTION100
6.003-8.4810.243530.222826X-RAY DIFFRACTION100

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