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- PDB-8gdn: Structure of PmHMGR bound to mevalonate, CoA and NAD. -

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Basic information

Entry
Database: PDB / ID: 8gdn
TitleStructure of PmHMGR bound to mevalonate, CoA and NAD.
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsSTRUCTURAL PROTEIN / Non-Rossmann fold / Homodimer / Reductase / HMG-CoA
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
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 / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas sp. 'mevalonii' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsPurohit, V. / Steussy, C.N. / Stauffacher, C.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM111645 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30 CA023168 United States
CitationJournal: Biophys.J. / Year: 2024
Title: pH-dependent reaction triggering in PmHMGR crystals for time-resolved crystallography.
Authors: Purohit, V. / Steussy, C.N. / Rosales, A.R. / Critchelow, C.J. / Schmidt, T. / Helquist, P. / Wiest, O. / Mesecar, A. / Cohen, A.E. / Stauffacher, C.V.
History
DepositionMar 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: 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)93,2008
Polymers91,2822
Non-polymers1,9176
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Electron density supports homodimerization of the enzyme monomer and binding of mentioned ligands.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-91 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.043, 226.043, 226.043
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


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 , 5 types, 484 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 54.43 %
Description: Dimensions - 226.7110 226.7110 226.7110 90.0000 90.0000 90.0000 Symm - I 41 3 2
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.2 M ammonium sulfate, 100 mM ADA and 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 67257 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.022 / Rrim(I) all: 0.094 / Χ2: 0.993 / Net I/σ(I): 8 / Num. measured all: 1095935
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.99-2.0613.12.97566310.30.6790.8463.0950.67899.9
2.06-2.1413.11.88166280.5390.8370.5381.9580.775100
2.14-2.2413.51.40266290.7760.9350.3951.4580.703100
2.24-2.3614.90.90466570.8710.9650.2420.9360.881100
2.36-2.5115.60.54566670.9510.9870.1420.5640.766100
2.51-2.716.30.36266810.9780.9940.0920.3740.899100
2.7-2.9718.90.267210.9930.9980.0470.2051.044100
2.97-3.419.20.12167430.9970.9990.0280.1251.235100
3.4-4.2919.60.07168020.99910.0160.0731.508100
4.29-5018.40.0417098110.010.0431.058100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.19 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 2823 5.08 %
Rwork0.1808 --
obs0.183 55594 82.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→48.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5945 0 122 478 6545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086293
X-RAY DIFFRACTIONf_angle_d1.0738595
X-RAY DIFFRACTIONf_dihedral_angle_d10.377910
X-RAY DIFFRACTIONf_chiral_restr0.0581004
X-RAY DIFFRACTIONf_plane_restr0.0091118
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.401330.281453X-RAY DIFFRACTION2
2.02-2.060.326100.3398211X-RAY DIFFRACTION7
2.06-2.10.2412260.2921636X-RAY DIFFRACTION20
2.1-2.140.27761090.26551944X-RAY DIFFRACTION62
2.14-2.190.27241520.24852892X-RAY DIFFRACTION92
2.19-2.240.30941650.26613000X-RAY DIFFRACTION96
2.24-2.30.35991630.30513034X-RAY DIFFRACTION96
2.3-2.360.24431560.21643145X-RAY DIFFRACTION99
2.36-2.430.27141540.19743129X-RAY DIFFRACTION99
2.43-2.510.25722140.20093054X-RAY DIFFRACTION99
2.51-2.60.25891650.20383117X-RAY DIFFRACTION99
2.6-2.70.22841890.20823088X-RAY DIFFRACTION98
2.7-2.820.24461460.19763121X-RAY DIFFRACTION98
2.82-2.970.2271710.19263108X-RAY DIFFRACTION97
2.97-3.160.26541870.18793087X-RAY DIFFRACTION97
3.16-3.40.20591560.1723113X-RAY DIFFRACTION98
3.4-3.740.18221480.15073177X-RAY DIFFRACTION98
3.75-4.290.19551520.13273198X-RAY DIFFRACTION98
4.29-5.40.16521770.13723234X-RAY DIFFRACTION99
5.4-48.190.20411800.16573430X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 88.4342 Å / Origin y: 129.1362 Å / Origin z: 118.6944 Å
111213212223313233
T0.1405 Å20.0691 Å20.0345 Å2-0.1645 Å2-0.0466 Å2--0.2393 Å2
L0.6831 °20.0643 °2-0.0898 °2-0.778 °20.2119 °2--0.7853 °2
S-0.0095 Å °-0.0016 Å °0.1716 Å °0.0089 Å °-0.0602 Å °0.1547 Å °-0.0921 Å °-0.0854 Å °0.042 Å °
Refinement TLS groupSelection details: all

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