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- PDB-9dcp: Structure of PmHMGR bound to mevalonate, CoA and NAD 1 minute aft... -

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Basic information

Entry
Database: PDB / ID: 9dcp
TitleStructure of PmHMGR bound to mevalonate, CoA and NAD 1 minute after reaction initiation at pH 9
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsOXIDOREDUCTASE/SUBSTRATE/INTERMEDIATE / Complex / reaction intermediate / Enzyme / OXIDOREDUCTASE / OXIDOREDUCTASE-SUBSTRATE-INTERMEDIATE complex
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADH) activity / hydroxymethylglutaryl-CoA reductase / hydroxymethylglutaryl-CoA reductase (NADPH) activity / coenzyme A metabolic process
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
: / COENZYME A / (R)-MEVALONATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas sp. 'mevalonii' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsPurohit, V. / Stauffacher, C.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM111645 United States
CitationJournal: To Be Published
Title: Watching Pseudomonas mevalonii HMG-CoA Reductase in Action
Authors: Patel, H. / Purohit, V. / Steussy, C.S. / Stauffacher, C.V. / Helquist, P. / Wiest, O. / Schmidt, T. / Rushton, P.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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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)94,4408
Polymers91,2822
Non-polymers3,1576
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: Determine via size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.766, 225.766, 225.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

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Protein , 1 types, 2 molecules AB

#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 sp. 'mevalonii' (bacteria) / Gene: mvaA / Plasmid: pKK-RED
Details (production host): Contained the mva operon in the expression vector pKK177-3
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P13702, hydroxymethylglutaryl-CoA reductase

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Non-polymers , 6 types, 290 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1AFY / (R)-mevaldehyde / (3R)-3-hydroxy-3-methyl-5-oxopentanoic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H11O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.2 M ammonium sulfate, 100 mM N-(2-acetamido)iminodiacetic acid, and 10% glycerol. Crystals were buffer exchanged into 1.2 M ammonium acetate, 100 mM ADA, and 10% PEG-400 buffer at pH 6.7 ...Details: 1.2 M ammonium sulfate, 100 mM N-(2-acetamido)iminodiacetic acid, and 10% glycerol. Crystals were buffer exchanged into 1.2 M ammonium acetate, 100 mM ADA, and 10% PEG-400 buffer at pH 6.7 (pH-jump buffer), followed by soaking with 1 mM NAD, mevalonate, and CoA in the pH-jump buffer for 1 minute at pH 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 58699 / % possible obs: 100 % / Redundancy: 31.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.029 / Rrim(I) all: 0.165 / Χ2: 1.115 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.08-2.1525.14.23657690.3010.680.8594.3230.875
2.15-2.2427.92.75957890.7070.910.532.810.913
2.24-2.3430.61.64857820.8570.9610.31.6750.975
2.34-2.4734.31.03858190.9390.9840.1791.0540.962
2.47-2.6233.80.67758250.9720.9930.1180.6871.007
2.62-2.8232.90.42658280.9880.9970.0750.4331.101
2.82-3.1131.70.25358560.9940.9990.0450.2571.186
3.11-3.5630.90.14658970.9980.9990.0260.1491.336
3.56-4.4833.10.10159280.99910.0180.1021.536
4.48-5030.50.07162060.99810.0130.0731.17

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→48.13 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 2723 5.04 %
Rwork0.2137 --
obs0.2151 54015 89.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 204 284 6392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036265
X-RAY DIFFRACTIONf_angle_d0.5378566
X-RAY DIFFRACTIONf_dihedral_angle_d17.5642226
X-RAY DIFFRACTIONf_chiral_restr0.041015
X-RAY DIFFRACTIONf_plane_restr0.0041101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.10.4886130.3993277X-RAY DIFFRACTION9
2.1-2.140.4499670.3821080X-RAY DIFFRACTION37
2.14-2.180.38481260.35732178X-RAY DIFFRACTION74
2.18-2.230.35651380.32792723X-RAY DIFFRACTION92
2.23-2.280.35731520.31812852X-RAY DIFFRACTION96
2.28-2.340.33881500.29742960X-RAY DIFFRACTION99
2.34-2.40.32451790.27942940X-RAY DIFFRACTION100
2.4-2.470.29291480.25862992X-RAY DIFFRACTION100
2.47-2.550.27311660.25382937X-RAY DIFFRACTION100
2.55-2.650.2931540.25352983X-RAY DIFFRACTION100
2.65-2.750.27931580.24032990X-RAY DIFFRACTION100
2.75-2.880.27111350.2372982X-RAY DIFFRACTION100
2.88-3.030.25941540.2372992X-RAY DIFFRACTION100
3.03-3.220.25591650.23173007X-RAY DIFFRACTION100
3.22-3.470.2471620.20313015X-RAY DIFFRACTION100
3.47-3.820.20331630.17883023X-RAY DIFFRACTION100
3.82-4.370.1961460.15213055X-RAY DIFFRACTION100
4.37-5.50.15931800.14993068X-RAY DIFFRACTION100
5.5-48.130.17131670.16413238X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 88.5288 Å / Origin y: 129.1286 Å / Origin z: 118.147 Å
111213212223313233
T0.1609 Å20.0565 Å20.0415 Å2-0.1829 Å2-0.136 Å2--0.6301 Å2
L0.5696 °20.0823 °20.0219 °2-0.6338 °20.3244 °2--0.6046 °2
S-0.1181 Å °-0.059 Å °0.3703 Å °0.0501 Å °-0.1973 Å °0.4391 Å °-0.1327 Å °-0.1275 Å °0.0068 Å °
Refinement TLS groupSelection details: all

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