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- PDB-3mp4: Crystal structure of Human lyase R41M mutant -

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Basic information

Entry
Database: PDB / ID: 3mp4
TitleCrystal structure of Human lyase R41M mutant
ComponentsHydroxymethylglutaryl-CoA lyase
KeywordsLYASE / Ketogenic enzyme / Human HMG-CoA lyase / R41M
Function / homology
Function and homology information


hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / Synthesis of Ketone Bodies / L-leucine catabolic process / peroxisomal matrix / mitochondrion organization / Peroxisomal protein import / lipid metabolic process / peroxisome ...hydroxymethylglutaryl-CoA lyase / hydroxymethylglutaryl-CoA lyase activity / ketone body biosynthetic process / Synthesis of Ketone Bodies / L-leucine catabolic process / peroxisomal matrix / mitochondrion organization / Peroxisomal protein import / lipid metabolic process / peroxisome / manganese ion binding / mitochondrial matrix / structural molecule activity / magnesium ion binding / protein-containing complex / mitochondrion / metal ion binding / cytosol
Similarity search - Function
Hydroxymethylglutaryl-CoA lyase, active site / Hydroxymethylglutaryl-coenzyme A lyase active site. / HMG-CoA lyase / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Hydroxymethylglutaryl-CoA lyase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFu, Z. / Runquist, J.A. / Montgomery, C. / Miziorko, H.M. / Kim, J.-J.P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Functional insights into human HMG-CoA lyase from structures of Acyl-CoA-containing ternary complexes.
Authors: Fu, Z. / Runquist, J.A. / Montgomery, C. / Miziorko, H.M. / Kim, J.J.
History
DepositionApr 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 6, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydroxymethylglutaryl-CoA lyase
B: Hydroxymethylglutaryl-CoA lyase
C: Hydroxymethylglutaryl-CoA lyase
D: Hydroxymethylglutaryl-CoA lyase
E: Hydroxymethylglutaryl-CoA lyase
F: Hydroxymethylglutaryl-CoA lyase


Theoretical massNumber of molelcules
Total (without water)189,3106
Polymers189,3106
Non-polymers00
Water6,882382
1
A: Hydroxymethylglutaryl-CoA lyase
B: Hydroxymethylglutaryl-CoA lyase


Theoretical massNumber of molelcules
Total (without water)63,1032
Polymers63,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-15 kcal/mol
Surface area22180 Å2
MethodPISA
2
C: Hydroxymethylglutaryl-CoA lyase
D: Hydroxymethylglutaryl-CoA lyase


Theoretical massNumber of molelcules
Total (without water)63,1032
Polymers63,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area22300 Å2
MethodPISA
3
E: Hydroxymethylglutaryl-CoA lyase
F: Hydroxymethylglutaryl-CoA lyase


Theoretical massNumber of molelcules
Total (without water)63,1032
Polymers63,1032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-15 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.490, 116.620, 86.980
Angle α, β, γ (deg.)90.00, 112.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Hydroxymethylglutaryl-CoA lyase / HMG-CoA lyase / HL / 3-hydroxy-3-methylglutarate-CoA lyase


Mass: 31551.631 Da / Num. of mol.: 6 / Mutation: R41M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMGCL / Plasmid: pTrc-HL1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105
References: UniProt: P35914, hydroxymethylglutaryl-CoA lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8K, Hepes buffer, MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2008 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→29.16 Å / Num. obs: 86402 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 37.8 Å2 / Rsym value: 0.051 / Net I/σ(I): 28.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5896 / % possible all: 64.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2cw6

2cw6


Resolution: 2.2→29.16 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 385823.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 8395 10 %RANDOM
Rwork0.219 ---
obs0.219 83541 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2952 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 46.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å210.35 Å2
2--8.04 Å20 Å2
3----5.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13049 0 0 382 13431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.367 502 9.5 %
Rwork0.331 4762 -
obs-4762 57.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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