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- PDB-1r7i: HMG-CoA Reductase from P. mevalonii, native structure at 2.2 angs... -

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Basic information

Entry
Database: PDB / ID: 1r7i
TitleHMG-CoA Reductase from P. mevalonii, native structure at 2.2 angstroms resolution.
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsOXIDOREDUCTASE / 4-ELECTRON OXIDO-REDUCTASE
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
Similarity search - Function
Hydroxymethylglutaryl-CoA reductase, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 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, bacterial-type / Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 3-hydroxy-3-methylglutaryl-coenzyme A Reductase; Chain A, domain 2 / 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. / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas mevalonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsWatson, J.M. / Steussy, C.N. / Burgner, J.W. / Lawrence, C.M. / Tabernero, L. / Rodwell, V.W. / Stauffacher, C.V.
CitationJournal: To be Published
Title: Structural Investigations of the Basis for Stereoselectivity from the Binary Complex of HMG-COA Reductase.
Authors: Watson, J.M. / Steussy, C.N. / Burgner, J.W. / Lawrence, C.M. / Tabernero, L. / Rodwell, V.W. / Stauffacher, C.V.
History
DepositionOct 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,7557
Polymers91,2822
Non-polymers4725
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10410 Å2
ΔGint-109 kcal/mol
Surface area26060 Å2
MethodPISA
2
A: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
hetero molecules

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

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)275,26521
Polymers273,8476
Non-polymers1,41715
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area38980 Å2
ΔGint-333 kcal/mol
Surface area70450 Å2
MethodPISA
3
A: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
B: 3-hydroxy-3-methylglutaryl-coenzyme A reductase
hetero molecules

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)183,51014
Polymers182,5654
Non-polymers94510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_456y-1/4,x+1/4,-z+5/41
Buried area22940 Å2
ΔGint-243 kcal/mol
Surface area50010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.186, 226.186, 226.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Detailsdeposited coordinates represent a homodimer. The biologically active multimeric structure is uncertain.

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Components

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


Mass: 45641.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mevalonii (bacteria) / Gene: MVAA / Production host: Escherichia coli (E. coli)
References: UniProt: P13702, hydroxymethylglutaryl-CoA reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: ADA, glycerol, ammonium sulfate, pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.21→26.66 Å / Num. all: 49914 / Num. obs: 43087 / % possible obs: 86.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.7 Å2
Reflection shellResolution: 2.2→2.3 Å / % possible all: 69.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→26.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 646813.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3489 8.1 %RANDOM
Rwork0.256 ---
obs0.256 43087 87 %-
all-49914 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 80.0361 Å2 / ksol: 0.389686 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.21→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 27 263 5833
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d1.51
X-RAY DIFFRACTIONc_mcbond_it2.311.5
X-RAY DIFFRACTIONc_mcangle_it3.612
X-RAY DIFFRACTIONc_scbond_it3.892
X-RAY DIFFRACTIONc_scangle_it5.532.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 464 8.2 %
Rwork0.305 5219 -
obs-5219 69.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4LIGANDS.PARLIGANDS.TOP

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