[English] 日本語
Yorodumi
- PDB-2iik: Crystal Structure of human peroxisomal acetyl-CoA acyl transferas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2iik
TitleCrystal Structure of human peroxisomal acetyl-CoA acyl transferase 1 (ACAA1)
Components3-ketoacyl-CoA thiolase, peroxisomalThiolase
KeywordsTRANSFERASE / FATTY ACID METABOLISM / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


palmitoyl-CoA oxidase activity / TYSND1 cleaves peroxisomal proteins / acetyl-CoA C-myristoyltransferase activity / protein targeting to peroxisome / fatty acid beta-oxidation using acyl-CoA oxidase / alpha-linolenic acid metabolic process / alpha-linolenic acid (ALA) metabolism / acetate CoA-transferase activity / acetyl-CoA C-acyltransferase / Beta-oxidation of very long chain fatty acids ...palmitoyl-CoA oxidase activity / TYSND1 cleaves peroxisomal proteins / acetyl-CoA C-myristoyltransferase activity / protein targeting to peroxisome / fatty acid beta-oxidation using acyl-CoA oxidase / alpha-linolenic acid metabolic process / alpha-linolenic acid (ALA) metabolism / acetate CoA-transferase activity / acetyl-CoA C-acyltransferase / Beta-oxidation of very long chain fatty acids / acetyl-CoA C-acyltransferase activity / very long-chain fatty acid metabolic process / neutrophil degranulation / phenylacetate catabolic process / bile acid metabolic process / fatty acid beta-oxidation / peroxisomal matrix / Peroxisomal protein import / peroxisome / specific granule lumen / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular region / membrane / cytosol
Similarity search - Function
Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal ...Thiolase, active site / Thiolases active site. / Thiolase, acyl-enzyme intermediate active site / Thiolases acyl-enzyme intermediate signature. / Thiolase, conserved site / Thiolases signature 2. / Thiolase / Thiolase, C-terminal / Thiolase, C-terminal domain / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-ketoacyl-CoA thiolase, peroxisomal
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPapagrigoriou, E. / Johansson, C. / Smee, C. / Kavanagh, K. / Pike, A.C.W. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Gileadi, O. ...Papagrigoriou, E. / Johansson, C. / Smee, C. / Kavanagh, K. / Pike, A.C.W. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of human peroxisomal acetyl-CoA acyl transferase 1 (ACAA1)
Authors: Papagrigoriou, E. / Johansson, C. / Smee, C. / Kavanagh, K. / Pike, A.C.W. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, ...Authors: Papagrigoriou, E. / Johansson, C. / Smee, C. / Kavanagh, K. / Pike, A.C.W. / Sundstrom, M. / Weigelt, J. / Edwards, A. / Arrowsmith, C.H. / Gileadi, O. / Gorrec, F. / Umeano, C. / von Delft, F. / Oppermann, U. / Structural Genomics Consortium (SGC)
History
DepositionSep 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-ketoacyl-CoA thiolase, peroxisomal
B: 3-ketoacyl-CoA thiolase, peroxisomal


Theoretical massNumber of molelcules
Total (without water)87,9382
Polymers87,9382
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-18 kcal/mol
Surface area26630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.147, 96.845, 142.055
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA47 - 15541 - 149
21ALAALALEULEUBB47 - 15541 - 149
32THRTHRVALVALAA166 - 231159 - 224
42THRTHRVALVALBB166 - 231159 - 224
53SERSERGLUGLUAA240 - 421233 - 414
63SERSERGLUGLUBB240 - 421233 - 414

-
Components

#1: Protein 3-ketoacyl-CoA thiolase, peroxisomal / Thiolase / Beta- ketothiolase / Acetyl-CoA acyltransferase / Peroxisomal 3-oxoacyl-CoA thiolase


Mass: 43969.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAA1 / Plasmid: pNIC28-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09110, acetyl-CoA C-acyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Amonium Sulphate, 0.1M Hepes, 25% PEG3350., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jul 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→80.06 Å / Num. all: 25624 / Num. obs: 25358 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.66 % / Rmerge(I) obs: 0.1099 / Net I/σ(I): 9.65
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 2.79 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.17 / Num. unique all: 2760 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MLPHAREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C7Z

2c7z


Resolution: 2.55→80.06 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.811 / SU ML: 0.198 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.527 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22345 1274 5 %RANDOM
Rwork0.17869 ---
obs0.18108 24037 99 %-
all-25624 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.615 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--1.76 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.55→80.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5639 0 0 226 5865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225718
X-RAY DIFFRACTIONr_bond_other_d0.0020.023798
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9817752
X-RAY DIFFRACTIONr_angle_other_deg1.19239355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.37524.619197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78215943
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9361534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021038
X-RAY DIFFRACTIONr_nbd_refined0.2170.21201
X-RAY DIFFRACTIONr_nbd_other0.1950.23970
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22903
X-RAY DIFFRACTIONr_nbtor_other0.0890.23049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2247
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.54009
X-RAY DIFFRACTIONr_mcbond_other0.141.51608
X-RAY DIFFRACTIONr_mcangle_it0.73326208
X-RAY DIFFRACTIONr_scbond_it1.51631914
X-RAY DIFFRACTIONr_scangle_it2.3144.51544
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2086tight positional0.040.05
2135loose positional0.275
2086tight thermal0.080.5
2135loose thermal0.7410
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 86 -
Rwork0.242 1702 -
obs--95.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5671-0.0271-0.08370.94940.29241.8841-0.0289-0.17690.01950.1663-0.02060.0226-0.07330.01740.0495-0.08690.00850.0054-0.10020.0199-0.10236.1548-7.0898-20.068
21.6416-0.1882-0.28520.8699-0.18541.6313-0.00630.1493-0.0469-0.1815-0.05660.0841-0.04240.04940.063-0.0939-0.0039-0.0251-0.0987-0.0239-0.084-5.504-8.9773-49.4576
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA33 - 42327 - 416
2X-RAY DIFFRACTION2BB21 - 42315 - 416

+
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://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