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- PDB-6eev: Structure of class II HMG-CoA reductase from Delftia acidovorans ... -

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Basic information

Entry
Database: PDB / ID: 6eev
TitleStructure of class II HMG-CoA reductase from Delftia acidovorans with mevalonate bound
Components3-hydroxy-3-methylglutaryl coenzyme A reductase
KeywordsOXIDOREDUCTASE / Mevalonate pathway
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process / ergosterol biosynthetic process / isoprenoid biosynthetic process / peroxisomal membrane / nucleotide binding
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / 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
sucrose / (R)-MEVALONATE / 3-hydroxy-3-methylglutaryl coenzyme A reductase
Similarity search - Component
Biological speciesDelftia acidovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsRagwan, E.R. / Arai, E. / Kung, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM116029 United States
CitationJournal: Biochemistry / Year: 2018
Title: New Crystallographic Snapshots of Large Domain Movements in Bacterial 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase.
Authors: Ragwan, E.R. / Arai, E. / Kung, Y.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4038
Polymers45,1911
Non-polymers1,2127
Water7,332407
1
A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules

A: 3-hydroxy-3-methylglutaryl coenzyme A reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,80616
Polymers90,3822
Non-polymers2,42414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area12610 Å2
ΔGint-115 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.370, 100.370, 75.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

21A-828-

HOH

31A-971-

HOH

41A-976-

HOH

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Components

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Protein / Sugars , 2 types, 3 molecules A

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


Mass: 45190.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Delftia acidovorans (bacteria) / Gene: Daci_0287 / Production host: Escherichia coli (E. coli)
References: UniProt: A9BQX8, hydroxymethylglutaryl-CoA reductase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 412 molecules

#3: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, pH 6.5, 600 mM lithium sulfate, 19% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2018
RadiationMonochromator: Cryo-Cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.49→57.125 Å / Num. obs: 70102 / % possible obs: 97.6 % / Redundancy: 3.8 % / Net I/σ(I): 10.5
Reflection shellResolution: 1.49→1.52 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→57.125 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.34
RfactorNum. reflection% reflection
Rfree0.1646 3540 5.05 %
Rwork0.1351 --
obs0.1366 70070 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.49→57.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2733 0 77 407 3217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052862
X-RAY DIFFRACTIONf_angle_d0.8213905
X-RAY DIFFRACTIONf_dihedral_angle_d19.91046
X-RAY DIFFRACTIONf_chiral_restr0.069471
X-RAY DIFFRACTIONf_plane_restr0.005504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.51040.26321210.21312715X-RAY DIFFRACTION100
1.5104-1.5320.21511480.19472716X-RAY DIFFRACTION99
1.532-1.55490.20541490.17692660X-RAY DIFFRACTION99
1.5549-1.57920.21291430.16422495X-RAY DIFFRACTION93
1.5792-1.60510.20551710.17052620X-RAY DIFFRACTION99
1.6051-1.63280.25631360.15972729X-RAY DIFFRACTION100
1.6328-1.66240.18181510.14932690X-RAY DIFFRACTION100
1.6624-1.69440.20671570.14562731X-RAY DIFFRACTION100
1.6944-1.7290.2011040.14362738X-RAY DIFFRACTION99
1.729-1.76660.1841370.14042706X-RAY DIFFRACTION99
1.7666-1.80770.18661380.13032693X-RAY DIFFRACTION99
1.8077-1.85290.15911430.12652628X-RAY DIFFRACTION96
1.8529-1.9030.16571080.12232555X-RAY DIFFRACTION93
1.903-1.9590.17031560.13482698X-RAY DIFFRACTION99
1.959-2.02230.16161810.132668X-RAY DIFFRACTION99
2.0223-2.09450.17531610.12732693X-RAY DIFFRACTION99
2.0945-2.17840.15881410.12082685X-RAY DIFFRACTION99
2.1784-2.27750.15921460.12132688X-RAY DIFFRACTION99
2.2775-2.39760.15791220.11952492X-RAY DIFFRACTION90
2.3976-2.54780.14531410.12692670X-RAY DIFFRACTION97
2.5478-2.74460.16431240.13922723X-RAY DIFFRACTION98
2.7446-3.02070.1651500.13632669X-RAY DIFFRACTION97
3.0207-3.45780.1602980.13932579X-RAY DIFFRACTION91
3.4578-4.35620.12381470.1152658X-RAY DIFFRACTION95
4.3562-57.16690.15871670.1432631X-RAY DIFFRACTION91

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