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- PDB-1qax: TERNARY COMPLEX OF PSEUDOMONAS MEVALONII HMG-COA REDUCTASE WITH H... -

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Basic information

Entry
Database: PDB / ID: 1qax
TitleTERNARY COMPLEX OF PSEUDOMONAS MEVALONII HMG-COA REDUCTASE WITH HMG-COA AND NAD+
ComponentsPROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
KeywordsOXIDOREDUCTASE / 4-ELECTRON OXIDO-REDUCTASE
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) activity => GO:0004420 / 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-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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxy-3-methylglutaryl-coenzyme A reductase / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesPseudomonas mevalonii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTabernero, L. / Bochar, D.A. / Rodwell, V.W. / Stauffacher, C.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase.
Authors: Tabernero, L. / Bochar, D.A. / Rodwell, V.W. / Stauffacher, C.V.
History
DepositionApr 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
B: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8534
Polymers91,2822
Non-polymers1,5702
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13640 Å2
ΔGint-67 kcal/mol
Surface area27280 Å2
MethodPISA
2
A: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
B: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
hetero molecules

A: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
B: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
hetero molecules

A: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
B: PROTEIN (3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)278,55812
Polymers273,8476
Non-polymers4,7106
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area47450 Å2
ΔGint-220 kcal/mol
Surface area75300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.700, 228.700, 228.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein 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 mevalonii (bacteria) / Gene: MVAA / Production host: Escherichia coli (E. coli) / References: UniProt: MVAA_PSEMV, UniProt: P13702*PLUS
#2: Chemical ChemComp-HMG / 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / (S)-HMG-COA


Mass: 906.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H39N7O20P3S
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growpH: 6.7
Details: VAPOR DIFFUSION, SITTING DROP, 295K, PH 6.7, 1.2M AMMONIUM SULFATE, 100MM ADA BUFFER
Crystal grow
*PLUS
pH: 8.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
2400 mM1dropKCl
310 %glycerol1drop
41.2 Mammonium sulfate1reservoir
575 mMsodium citrate1reservoir
6100 mMsodium ADA1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 23346 / % possible obs: 92.2 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.3 / % possible all: 64.6
Reflection shell
*PLUS
% possible obs: 64.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementResolution: 2.8→8 Å
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1794 -RANDOM
Rwork0.215 ---
obs0.194 21515 84.2 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5934 0 102 71 6107
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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