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- PDB-8vlq: Structure of PmHMGR bound to mevalonate, CoA and NAD 5 minutes af... -

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Basic information

Entry
Database: PDB / ID: 8vlq
TitleStructure of PmHMGR bound to mevalonate, CoA and NAD 5 minutes after reaction initiation at pH 9
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 (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 / 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: 2.07 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
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)94,6829
Polymers91,2822
Non-polymers3,3997
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14840 Å2
ΔGint-93 kcal/mol
Surface area26260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.988, 225.988, 225.988
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 , 8 types, 436 molecules

#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-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: 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
#8: Chemical ChemComp-MEV / (R)-MEVALONATE


Mass: 147.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11O4 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Description: Dimensions - 225.988 225.988 225.988 90.00 90.00 90.00 Symmetry - I 41 3 2
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

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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: 60173 / % possible obs: 99.1 % / Redundancy: 9.5 % / Biso Wilson estimate: 23.45 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1054 / Rpim(I) all: 0.03596 / Rsym value: 0.1114 / Net I/av σ(I): 20.44 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.06-2.138.50.75954730.6070.8690.2850.8131.00591.3
2.13-2.22100.46859520.9380.9840.1560.4930.513100
2.22-2.329.70.44859900.9310.9820.1520.4731.17100
2.32-2.449.40.21260150.9840.9960.0720.2240.578100
2.44-2.69.70.14860050.9920.9980.050.1560.661100
2.6-2.89.80.12260470.9940.9990.0410.1290.986100
2.8-3.089.30.08160510.9960.9990.0280.0861.089100
3.08-3.529.90.06760770.9980.9990.0220.0711.556100
3.52-4.449.50.05361530.99810.0180.0561.957100
4.44-509.20.03964100.99910.0130.0411.27299.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→48.18 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 2994 5.05 %
Rwork0.2151 --
obs0.2167 59238 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.07→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 219 429 6558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036280
X-RAY DIFFRACTIONf_angle_d0.5958579
X-RAY DIFFRACTIONf_dihedral_angle_d9.009911
X-RAY DIFFRACTIONf_chiral_restr0.041000
X-RAY DIFFRACTIONf_plane_restr0.0041108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.10.36611140.35452179X-RAY DIFFRACTION81
2.1-2.140.33561400.31712618X-RAY DIFFRACTION98
2.14-2.170.34421640.30922659X-RAY DIFFRACTION100
2.17-2.220.35091410.30672668X-RAY DIFFRACTION100
2.22-2.260.35811290.35532577X-RAY DIFFRACTION96
2.26-2.310.34981430.30912613X-RAY DIFFRACTION98
2.31-2.360.28041450.26922690X-RAY DIFFRACTION100
2.36-2.420.33121540.26062657X-RAY DIFFRACTION100
2.42-2.490.27271300.25412712X-RAY DIFFRACTION100
2.49-2.560.2621570.24192682X-RAY DIFFRACTION100
2.56-2.640.30041400.24132698X-RAY DIFFRACTION100
2.64-2.740.27541470.232678X-RAY DIFFRACTION100
2.74-2.850.23961140.22372732X-RAY DIFFRACTION100
2.85-2.980.24811400.21482703X-RAY DIFFRACTION100
2.98-3.140.22961460.21642706X-RAY DIFFRACTION100
3.14-3.330.25551510.21122715X-RAY DIFFRACTION100
3.33-3.590.20931450.18492727X-RAY DIFFRACTION100
3.59-3.950.23141390.16882744X-RAY DIFFRACTION100
3.95-4.520.19821470.14922775X-RAY DIFFRACTION100
4.53-5.690.17071550.15962766X-RAY DIFFRACTION100
5.7-48.180.20821530.17252945X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 88.424 Å / Origin y: 129.1591 Å / Origin z: 118.4248 Å
111213212223313233
T0.0328 Å20.1379 Å20.0796 Å2-0.0515 Å2-0.1835 Å2--0.5217 Å2
L0.1811 °20.0237 °20.0483 °2-0.2113 °20.177 °2--0.2524 °2
S-0.123 Å °-0.039 Å °0.2865 Å °0.0892 Å °-0.1774 Å °0.4014 Å °-0.1117 Å °-0.1263 Å °-0.1163 Å °
Refinement TLS groupSelection details: all

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