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- PDB-6hr7: HMG-CoA reductase from Methanothermococcus thermolithotrophicus a... -

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Basic information

Entry
Database: PDB / ID: 6hr7
TitleHMG-CoA reductase from Methanothermococcus thermolithotrophicus apo form at 2.4 A resolution
ComponentsHMG-CoA reductase
KeywordsOXIDOREDUCTASE / HMG-CoA / Mevalonate biosynthesis / statins / cholesterol biosynthesis / isoprenoids / structural rearrangement.
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / sterol biosynthetic process / coenzyme A metabolic process / isoprenoid biosynthetic process / nucleotide binding
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / 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, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / Hydroxymethylglutaryl-coenzyme A reductases signature 2. / Hydroxymethylglutaryl-coenzyme A reductases signature 1. / 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. / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 3-hydroxy-3-methylglutaryl coenzyme A reductase
Similarity search - Component
Biological speciesMethanothermococcus thermolithotrophicus DSM 2095 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWagner, T. / Voegeli, B. / Erb, T.J. / Shima, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Febs Lett. / Year: 2019
Title: Crystal structure of archaeal HMG-CoA reductase: insights into structural changes of the C-terminal helix of the class-I enzyme.
Authors: Vogeli, B. / Shima, S. / Erb, T.J. / Wagner, T.
History
DepositionSep 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: HMG-CoA reductase
B: HMG-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,67715
Polymers93,2762
Non-polymers1,40213
Water73941
1
A: HMG-CoA reductase
B: HMG-CoA reductase
hetero molecules

A: HMG-CoA reductase
B: HMG-CoA reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,35530
Polymers186,5514
Non-polymers2,80426
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
Buried area32590 Å2
ΔGint-309 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.322, 83.322, 211.212
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HMG-CoA reductase


Mass: 46637.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: /
Source: (gene. exp.) Methanothermococcus thermolithotrophicus DSM 2095 (archaea)
Tissue: / / Cell: / / Cell line: / / Gene: HMGR / Organ: / / Plasmid: pET-28b / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21 (bacteria) / Tissue (production host): / / Variant (production host): BL21-AI
References: UniProt: A0A4V8GZY0*PLUS, hydroxymethylglutaryl-CoA reductase (NADPH)

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Non-polymers , 7 types, 54 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.27 Å3/Da / Density % sol: 45.91 % / Description: Long rod shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: HMGR was concentrated until 10 mg/ml by using an Amicon Ultra-4 Centrifugation filter (30 kDa cut-off) (Millipore) and centrifuged for 5 minute to remove any aggregates and dust. 0.7 ul of ...Details: HMGR was concentrated until 10 mg/ml by using an Amicon Ultra-4 Centrifugation filter (30 kDa cut-off) (Millipore) and centrifuged for 5 minute to remove any aggregates and dust. 0.7 ul of protein sample was spotted on a 96-well 2-drop MRC Crystallization Plates (Molecular Dimensions, Suffolk, UK) and 0.7 ul of reservoir solution was mixed. The best crystals were obtained after several month using a solution containing 40% v/v PEG 400, 100 mM Tris PH 8.5 and 200 mM Li2SO4.
Temp details: Temperature fluctation of +/- 3 degree

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97662 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97662 Å / Relative weight: 1
ReflectionResolution: 2.4→42.613 Å / Num. obs: 33184 / % possible obs: 99.7 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.029 / Rrim(I) all: 0.094 / Net I/σ(I): 16.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.8 % / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4821 / CC1/2: 0.634 / Rpim(I) all: 0.375 / Rrim(I) all: 1.236 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDS3.3.22data reduction
SCALAdata scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DQ8

1dq8


Resolution: 2.4→42.613 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2198 1631 4.92 %
Rwork0.1727 --
obs0.1752 33130 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 68.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6050 0 69 41 6160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076189
X-RAY DIFFRACTIONf_angle_d0.8438332
X-RAY DIFFRACTIONf_dihedral_angle_d17.9733755
X-RAY DIFFRACTIONf_chiral_restr0.054977
X-RAY DIFFRACTIONf_plane_restr0.0051050
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47060.3646990.2762628X-RAY DIFFRACTION100
2.4706-2.55030.31311320.24482599X-RAY DIFFRACTION100
2.5503-2.64150.28921050.21292645X-RAY DIFFRACTION100
2.6415-2.74720.25181520.20272583X-RAY DIFFRACTION100
2.7472-2.87220.2661390.2052622X-RAY DIFFRACTION100
2.8722-3.02360.23681320.20772562X-RAY DIFFRACTION99
3.0236-3.2130.23141570.17812628X-RAY DIFFRACTION100
3.213-3.4610.22991310.17142620X-RAY DIFFRACTION100
3.461-3.80910.20621310.16212642X-RAY DIFFRACTION100
3.8091-4.35980.20561430.14412632X-RAY DIFFRACTION100
4.3598-5.4910.19871460.1512638X-RAY DIFFRACTION100
5.491-42.61930.20241640.16972700X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0743-0.0066-0.04620.0419-0.0120.0312-0.2599-0.4199-0.77560.32030.14830.4540.5791-0.4824-0.00321.20890.06230.07570.53970.04770.783210.946613.706783.1802
21.2046-0.24160.08210.4247-0.66941.2948-0.4088-0.1574-0.39960.05440.0913-0.16171.19680.7185-0.52120.6950.41280.0490.75990.13220.599630.361628.952589.4032
31.464-0.1617-0.63710.62430.33262.6129-0.1125-0.1396-0.08250.18630.0265-0.09030.47230.7284-0.01130.45890.1464-0.05770.56590.12830.524727.85244.9482108.7465
40.03130.0175-0.02010.0416-0.01210.01180.2140.52910.045-0.11670.0313-0.5044-0.71870.2334-0.0020.79040.20090.01411.85140.17631.017457.205539.852285.1667
50.9228-0.63190.39961.0380.48582.1066-0.19650.1178-0.10360.15660.0703-0.04750.64150.6472-0.03460.60160.2030.03450.68030.11810.468326.06934.854985.9133
60.68480.2148-0.18151.41860.7592.4349-0.07420.08070.0974-0.1357-0.1138-0.0225-0.120.2158-0.00030.35010.0419-0.05280.41850.14440.503816.123452.238389.3833
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 401 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 27 )
5X-RAY DIFFRACTION5chain 'B' and (resid 28 through 133 )
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 400 )

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