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- PDB-5wpk: Structure of the class II 3-hydroxy-3-methylglutaryl-CoA reductas... -

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Basic information

Entry
Database: PDB / ID: 5wpk
TitleStructure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus pneumoniae bound to HMG-CoA and in a partially closed conformation
Components3-hydroxy-3-methylglutaryl coenzyme A reductase
KeywordsOXIDOREDUCTASE / 3-hydroxy-3-methylglutaryl-CoA reductase / HMG-CoA / conformational change
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / nucleotide binding
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / 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 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, bacterial-type / 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 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. / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / 3-hydroxy-3-methylglutaryl coenzyme A reductase / 3-hydroxy-3-methylglutaryl coenzyme A reductase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiller, B.R. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116029 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Features and Domain Movements Controlling Substrate Binding and Cofactor Specificity in Class II HMG-CoA Reductase.
Authors: Miller, B.R. / Kung, Y.
History
DepositionAug 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7149
Polymers92,9162
Non-polymers2,7987
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13870 Å2
ΔGint-40 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.865, 131.248, 57.957
Angle α, β, γ (deg.)90.00, 102.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 46457.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria)
Gene: mvaA, mvaA_1, mvaA_3, AWW74_09880, ERS019416_00185, ERS019687_00346, ERS020135_00205, ERS020138_01692, ERS020141_01867, ERS020145_01986, ERS020146_01579, ERS020155_00051, ERS020158_01777, ...Gene: mvaA, mvaA_1, mvaA_3, AWW74_09880, ERS019416_00185, ERS019687_00346, ERS020135_00205, ERS020138_01692, ERS020141_01867, ERS020145_01986, ERS020146_01579, ERS020155_00051, ERS020158_01777, ERS020520_02006, ERS020525_01644, ERS020528_00536, ERS020531_01915, ERS020532_00514, ERS020539_01756, ERS020726_02213, ERS020726_02223, ERS020822_01277, ERS021354_03805, ERS021629_07183, ERS021733_05462, ERS232524_02161, ERS367337_00780, ERS409444_00519
Plasmid: pSKB3
Details (production host): N-terminal hexa-his-tag with kanomycin cassette
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0D6J7E8, UniProt: Q8DNS5*PLUS, hydroxymethylglutaryl-CoA reductase (NADPH)
#2: Chemical ChemComp-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 100-250 mM lithium sulfate, 15-25% PEG4000
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2017
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.3→19.241 Å / Num. obs: 36792 / % possible obs: 98.17 % / Redundancy: 3.5 % / CC1/2: 0.987 / Rmerge(I) obs: 0.1514 / Net I/σ(I): 6.48
Reflection shellResolution: 2.3→2.382 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5832 / Mean I/σ(I) obs: 1.84 / Num. unique obs: 3643 / CC1/2: 0.676 / % possible all: 97.98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QAE

3qae


Resolution: 2.3→19.241 Å / Cross valid method: FREE R-VALUE / σ(F): 478.83 / Phase error: 27.84
RfactorNum. reflection% reflection
Rfree0.2333 1815 4.93 %
Rwork0.1771 --
obs0.187 36792 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.241 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 166 417 6603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036300
X-RAY DIFFRACTIONf_angle_d0.6278553
X-RAY DIFFRACTIONf_dihedral_angle_d6.7045142
X-RAY DIFFRACTIONf_chiral_restr0.042977
X-RAY DIFFRACTIONf_plane_restr0.0041102
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3003-2.36240.32341520.24522621X-RAY DIFFRACTION92
2.3624-2.43180.28691260.23242719X-RAY DIFFRACTION93
2.4318-2.51010.28531520.22582679X-RAY DIFFRACTION93
2.5101-2.59960.2721350.22662654X-RAY DIFFRACTION94
2.5996-2.70340.26821270.20882663X-RAY DIFFRACTION93
2.7034-2.82610.26591500.21132686X-RAY DIFFRACTION93
2.8261-2.97460.28141460.19862663X-RAY DIFFRACTION93
2.9746-3.16020.23211310.19392720X-RAY DIFFRACTION94
3.1602-3.40290.26541170.17832739X-RAY DIFFRACTION94
3.4029-3.74310.23831470.1682664X-RAY DIFFRACTION93
3.7431-4.27950.1741200.15362710X-RAY DIFFRACTION94
4.2795-5.37230.2091440.14662719X-RAY DIFFRACTION94
5.3723-19.24190.19931310.17582762X-RAY DIFFRACTION94

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