[English] 日本語
Yorodumi
- PDB-3mp5: Crystal Structure of Human Lyase R41M in complex with HMG-CoA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mp5
TitleCrystal Structure of Human Lyase R41M in complex with HMG-CoA
ComponentsHydroxymethylglutaryl-CoA lyase
KeywordsLYASE / Ketogenic enzyme / Human HMG-CoA Lyase / 3-Hydroxyl-3-methylglutaryl-CoA
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
3-HYDROXY-3-METHYLGLUTARYL-COENZYME A / Hydroxymethylglutaryl-CoA lyase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.25 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 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,2659
Polymers189,3106
Non-polymers9553
Water6,197344
1
A: Hydroxymethylglutaryl-CoA lyase
B: Hydroxymethylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0344
Polymers63,1032
Non-polymers9312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-18 kcal/mol
Surface area21960 Å2
MethodPISA
2
C: Hydroxymethylglutaryl-CoA lyase
D: Hydroxymethylglutaryl-CoA lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1283
Polymers63,1032
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-24 kcal/mol
Surface area22170 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 area2350 Å2
ΔGint-14 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.980, 116.660, 86.520
Angle α, β, γ (deg.)90.00, 112.16, 90.00
Int Tables number5
Space group name H-MC121

-
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: 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8K, Hepes buffer, MgCl2 and HMG-CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2007
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→28.35 Å / Num. obs: 86171 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 30.4 Å2 / Rsym value: 0.101 / Net I/σ(I): 15.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 8582 / Rsym value: 0.674 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3MP4

3mp4


Resolution: 2.25→28.35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 204339.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 8220 10 %RANDOM
Rwork0.221 ---
obs0.221 81864 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.8618 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å28.99 Å2
2--0.6 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13034 0 60 344 13438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it22
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.572.5
LS refinement shellResolution: 2.25→2.33 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.374 720 9.8 %
Rwork0.323 6631 -
obs-6631 85.6 %
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
X-RAY DIFFRACTION4hmg.parhmg.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more