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- PDB-1dqa: COMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH ... -

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Basic information

Entry
Database: PDB / ID: 1dqa
TitleCOMPLEX OF THE CATALYTIC PORTION OF HUMAN HMG-COA REDUCTASE WITH HMG, COA, AND NADP+
ComponentsPROTEIN (HMG-COA REDUCTASE)
KeywordsOXIDOREDUCTASE / CHOLESTEROL BIOSYNTHESIS / HMG-COA / NADPH
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / GTPase regulator activity / coenzyme A binding / negative regulation of amyloid-beta clearance / sterol biosynthetic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coenzyme A metabolic process / peroxisomal membrane ...hydroxymethylglutaryl-CoA reductase (NADPH) / hydroxymethylglutaryl-CoA reductase (NADPH) activity / GTPase regulator activity / coenzyme A binding / negative regulation of amyloid-beta clearance / sterol biosynthetic process / Cholesterol biosynthesis / EGR2 and SOX10-mediated initiation of Schwann cell myelination / coenzyme A metabolic process / peroxisomal membrane / isoprenoid biosynthetic process / cholesterol biosynthetic process / negative regulation of protein secretion / NADPH binding / regulation of ERK1 and ERK2 cascade / Activation of gene expression by SREBF (SREBP) / long-term synaptic potentiation / visual learning / PPARA activates gene expression / negative regulation of protein catabolic process / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
HMGR, N-terminal domain / HMGR, N-terminal domain / Hydroxymethylglutaryl-CoA reductase, metazoan / Hydroxymethylglutaryl-CoA reductase, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / 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. ...HMGR, N-terminal domain / HMGR, N-terminal domain / Hydroxymethylglutaryl-CoA reductase, metazoan / Hydroxymethylglutaryl-CoA reductase, eukaryotic/archaeal type / Hydroxymethylglutaryl-CoA reductase, N-terminal / 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. / : / Sterol-sensing domain of SREBP cleavage-activation / Sterol-sensing domain (SSD) profile. / Sterol-sensing domain / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
COENZYME A / 3-HYDROXY-3-METHYL-GLUTARIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-hydroxy-3-methylglutaryl-coenzyme A reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2 Å
AuthorsIstvan, E.S. / Palnitkar, M. / Buchanan, S.K. / Deisenhofer, J.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis.
Authors: Istvan, E.S. / Palnitkar, M. / Buchanan, S.K. / Deisenhofer, J.
History
DepositionDec 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (HMG-COA REDUCTASE)
B: PROTEIN (HMG-COA REDUCTASE)
C: PROTEIN (HMG-COA REDUCTASE)
D: PROTEIN (HMG-COA REDUCTASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,77816
Polymers200,0864
Non-polymers6,69212
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38160 Å2
ΔGint-156 kcal/mol
Surface area46400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.918, 172.630, 73.991
Angle α, β, γ (deg.)90.00, 117.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (HMG-COA REDUCTASE)


Mass: 50021.523 Da / Num. of mol.: 4 / Fragment: CATALYTIC PORTION / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX / Production host: Escherichia coli (E. coli)
References: UniProt: P04035, hydroxymethylglutaryl-CoA reductase (NADPH)
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-MAH / 3-HYDROXY-3-METHYL-GLUTARIC ACID


Mass: 162.141 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O5 / Comment: alkaloid*YM
#4: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.09 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5 / Details: pH 7.50
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112-15 %(w/v)PEG400011
230-50 mMdithiothreitol11
310 %glycerol11
40.1-0.2 Mammonium acetate11
530 mMNa-HEPES11
71 mMNADP+11
6(R,S)-HMG-CoA11molar ratio of 1:1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.083
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.083 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. obs: 109778 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 27.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.193 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
EPMRphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 2→44 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2186 2 %RANDOM
Rwork0.168 ---
obs0.168 109701 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.26 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.61 Å20 Å20.8 Å2
2--0.77 Å20 Å2
3---1.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12010 0 428 471 12909
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.46
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it2.542
X-RAY DIFFRACTIONc_scangle_it3.622.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.205 371 2.1 %
Rwork0.162 17197 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMLIG.TOP
X-RAY DIFFRACTION3CIS.PARAM
X-RAY DIFFRACTION4LIG.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.46

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