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- PDB-8sz6: PmHMGR bound to mevaldehyde and CoA -

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Basic information

Entry
Database: PDB / ID: 8sz6
TitlePmHMGR bound to mevaldehyde and CoA
Components3-hydroxy-3-methylglutaryl-coenzyme A reductase
KeywordsOXIDOREDUCTASE / Non-Rossmann fold / Homodimer / Reductase / HMG-CoA / STRUCTURAL PROTEIN
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-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
: / : / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas sp. 'mevalonii' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPurohit, V. / Stauffacher, C.V. / Steussy, C.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM111645 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
DepositionMay 27, 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)92,7458
Polymers91,2822
Non-polymers1,4626
Water13,980776
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 area10630 Å2
ΔGint-113 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.939, 225.939, 225.939
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-713-

HOH

21A-906-

HOH

31A-976-

HOH

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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 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
#2: Chemical ChemComp-ZKE / Mevaldyl-Coenzyme A / (3R,5R,9R,19R,21S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9,19,21-pentahydroxy-8,8,21-trimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-18-thia-11,15-diaza-3lambda~5~,5lambda~5~-diphosphatricosan-23-oic acid (non-preferred name)


Mass: 913.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46N7O20P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-XII / (3R)-3,5,5-trihydroxy-3-methylpentanoic acid


Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 776 / Source method: isolated from a natural source / Formula: H2O
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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 1.2 M ammonium sulfate, 100 mM N-(2-Acetamido)iminodiacetic acid and 10 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.65→28.69 Å / Num. obs: 116429 / % possible obs: 99.9 % / Redundancy: 9 % / CC1/2: 0.9 / CC star: 1 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.015 / Rrim(I) all: 0.044 / Χ2: 1.056 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.65-1.717.80.43115020.9190.9790.1630.460.867100
1.71-1.788.20.296115670.9630.9910.1090.3160.81100
1.78-1.868.60.19115360.9830.9960.0680.2020.799100
1.86-1.9690.135115410.9890.9970.0470.1430.883100
1.96-2.089.50.087115480.9950.9990.030.0920.873100
2.08-2.249.60.062116020.9970.9990.0210.0650.98100
2.24-2.469.60.047116340.99810.0160.0490.984100
2.46-2.829.60.038116840.99810.0130.041.126100
2.82-3.559.50.034117910.99910.0120.0361.333100
3.55-28.698.90.028120240.9970.9990.010.0291.8198.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.69 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1736 5843 5.02 %
Rwork0.1511 --
obs0.1523 116309 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→28.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 89 776 6459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165894
X-RAY DIFFRACTIONf_angle_d1.4498050
X-RAY DIFFRACTIONf_dihedral_angle_d14.9752149
X-RAY DIFFRACTIONf_chiral_restr0.101946
X-RAY DIFFRACTIONf_plane_restr0.0121059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.22061760.18783662X-RAY DIFFRACTION100
1.67-1.690.20241800.17163672X-RAY DIFFRACTION100
1.69-1.710.2032060.16883612X-RAY DIFFRACTION100
1.71-1.730.22921830.16433652X-RAY DIFFRACTION100
1.73-1.750.18171840.15933686X-RAY DIFFRACTION100
1.75-1.780.21991830.15693657X-RAY DIFFRACTION100
1.78-1.80.20212010.15583633X-RAY DIFFRACTION100
1.8-1.830.18732080.15293628X-RAY DIFFRACTION100
1.83-1.860.21492270.15833629X-RAY DIFFRACTION100
1.86-1.890.19051840.16373626X-RAY DIFFRACTION100
1.89-1.920.19061890.15893705X-RAY DIFFRACTION100
1.92-1.960.21511660.15553669X-RAY DIFFRACTION100
1.96-1.990.21431860.14993664X-RAY DIFFRACTION100
1.99-2.030.16512020.14793652X-RAY DIFFRACTION100
2.03-2.080.17432030.14713645X-RAY DIFFRACTION100
2.08-2.130.16071790.1533684X-RAY DIFFRACTION100
2.13-2.180.15222010.14553670X-RAY DIFFRACTION100
2.18-2.240.18432020.14713654X-RAY DIFFRACTION100
2.24-2.30.17361980.15683687X-RAY DIFFRACTION100
2.3-2.380.18462110.15153650X-RAY DIFFRACTION100
2.38-2.460.17781900.15353698X-RAY DIFFRACTION100
2.46-2.560.18882130.15423674X-RAY DIFFRACTION100
2.56-2.680.18621790.16093711X-RAY DIFFRACTION100
2.68-2.820.17422160.15493680X-RAY DIFFRACTION100
2.82-30.1592070.15273699X-RAY DIFFRACTION100
3-3.230.18111840.16153729X-RAY DIFFRACTION100
3.23-3.550.16981890.14483750X-RAY DIFFRACTION100
3.55-4.060.15152120.13493730X-RAY DIFFRACTION100
4.07-5.120.13861890.12613786X-RAY DIFFRACTION99
5.12-28.690.17351950.17083872X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 89.6256 Å / Origin y: 129.0348 Å / Origin z: 120.1406 Å
111213212223313233
T0.1269 Å20.0393 Å20.0162 Å2-0.1349 Å20.0072 Å2--0.1466 Å2
L0.3704 °2-0.0402 °2-0.0986 °2-0.4131 °20.141 °2--0.4983 °2
S0.0101 Å °0.0336 Å °0.0286 Å °-0.0464 Å °-0.0231 Å °0.0176 Å °-0.0383 Å °-0.0318 Å °0.0106 Å °
Refinement TLS groupSelection details: all

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