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

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Basic information

Entry
Database: PDB / ID: 5wpj
TitleStructure of the class II 3-hydroxy-3-methylglutaryl-CoA reductase from Streptococcus pneumoniae bound to NADPH in open conformations
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
Helicase, Ruva Protein; domain 3 - #660 / 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 ...Helicase, Ruva Protein; domain 3 - #660 / 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. / Helicase, Ruva Protein; domain 3 / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 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 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 / Derived calculations / Category: pdbx_audit_support / pdbx_struct_assembly_gen
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list
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

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl coenzyme A reductase
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
D: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,9459
Polymers185,8314
Non-polymers1,1145
Water29,7791653
1
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)93,8455
Polymers92,9162
Non-polymers9303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-65 kcal/mol
Surface area28180 Å2
MethodPISA
2
C: 3-hydroxy-3-methylglutaryl coenzyme A reductase
D: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1004
Polymers92,9162
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-62 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 84.000, 94.210
Angle α, β, γ (deg.)108.16, 100.60, 109.12
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 46457.820 Da / Num. of mol.: 4
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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1653 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 100-250 mM lithium sulfate, 30-40% 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: Apr 21, 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→72.72 Å / Num. obs: 95302 / % possible obs: 93.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.1159 / Net I/σ(I): 5.02
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.4474 / Mean I/σ(I) obs: 1.88 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QAE

3qae


Resolution: 2→72.72 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.7
RfactorNum. reflection% reflection
Rfree0.224 4683 4.91 %
Rwork0.164 --
obs0.167 95287 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→72.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11861 0 72 1653 13586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812183
X-RAY DIFFRACTIONf_angle_d1.24316552
X-RAY DIFFRACTIONf_dihedral_angle_d13.7554461
X-RAY DIFFRACTIONf_chiral_restr0.0471920
X-RAY DIFFRACTIONf_plane_restr0.0062159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02280.32451310.28132956X-RAY DIFFRACTION92
2.0228-2.04660.32491440.25853022X-RAY DIFFRACTION92
2.0466-2.07150.30591460.25273032X-RAY DIFFRACTION93
2.0715-2.09770.30511440.23723009X-RAY DIFFRACTION94
2.0977-2.12530.27221500.23163068X-RAY DIFFRACTION94
2.1253-2.15450.28931610.22063003X-RAY DIFFRACTION93
2.1545-2.18520.29721350.21233064X-RAY DIFFRACTION94
2.1852-2.21790.28911390.20583023X-RAY DIFFRACTION93
2.2179-2.25250.26011660.20613023X-RAY DIFFRACTION93
2.2525-2.28950.25931410.19863088X-RAY DIFFRACTION94
2.2895-2.32890.27071560.18363035X-RAY DIFFRACTION93
2.3289-2.37130.25881490.18822986X-RAY DIFFRACTION93
2.3713-2.41690.21421400.18093041X-RAY DIFFRACTION92
2.4169-2.46620.27391560.18262944X-RAY DIFFRACTION91
2.4662-2.51990.2361270.18012852X-RAY DIFFRACTION87
2.5199-2.57850.26491410.16873068X-RAY DIFFRACTION94
2.5785-2.6430.23641940.16233042X-RAY DIFFRACTION95
2.643-2.71440.23991660.16723016X-RAY DIFFRACTION94
2.7144-2.79430.23481700.16033058X-RAY DIFFRACTION94
2.7943-2.88450.24721780.15923046X-RAY DIFFRACTION95
2.8845-2.98760.22851750.15633057X-RAY DIFFRACTION95
2.9876-3.10720.20151410.15133039X-RAY DIFFRACTION94
3.1072-3.24860.2391680.15313062X-RAY DIFFRACTION94
3.2486-3.41990.21261590.14082974X-RAY DIFFRACTION92
3.4199-3.63420.20991600.13712800X-RAY DIFFRACTION87
3.6342-3.91480.17591620.12413016X-RAY DIFFRACTION94
3.9148-4.30870.14311580.11233117X-RAY DIFFRACTION97
4.3087-4.9320.16951610.11213135X-RAY DIFFRACTION96
4.932-6.21330.19661880.14453050X-RAY DIFFRACTION95
6.2133-72.7720.19161770.17052978X-RAY DIFFRACTION92

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