[English] 日本語
Yorodumi
- PDB-1qfl: BIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH A RE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qfl
TitleBIOSYNTHETIC THIOLASE FROM ZOOGLOEA RAMIGERA IN COMPLEX WITH A REACTION INTERMEDIATE.
ComponentsPROTEIN (ACETOACETYL-COA THIOLASE)
KeywordsTRANSFERASE / THIOLASE / COA / TETRAMERIZATION MOTIF / COVALENT INTERMEDIATE / ACETYL-CYSTEINE
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acetyl-CoA C-acetyltransferase / acetyl-CoA C-acetyltransferase activity / fatty acid beta-oxidation / 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
COENZYME A / Acetyl-CoA acetyltransferase
Similarity search - Component
Biological speciesZoogloea ramigera (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsModis, Y. / Wierenga, R.K.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: A biosynthetic thiolase in complex with a reaction intermediate: the crystal structure provides new insights into the catalytic mechanism.
Authors: Modis, Y. / Wierenga, R.K.
#1: Journal: Biochemistry / Year: 1989
Title: Mechanistic Studies on Beta-Ketoacyl Thiolase from Zoogloea Ramigera: Identification of the Active-Site Nucleophile as Cys89, its Mutation to Ser89, and Kinetic and Thermodynamic ...Title: Mechanistic Studies on Beta-Ketoacyl Thiolase from Zoogloea Ramigera: Identification of the Active-Site Nucleophile as Cys89, its Mutation to Ser89, and Kinetic and Thermodynamic Characterization of Wild-Type and Mutant Enzymes
Authors: Thompson, S. / Mayer, F. / Peoples, O.P. / Masamune, S. / Sinskey, A. / Walsh, C.T.
History
DepositionApr 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (ACETOACETYL-COA THIOLASE)
B: PROTEIN (ACETOACETYL-COA THIOLASE)
C: PROTEIN (ACETOACETYL-COA THIOLASE)
D: PROTEIN (ACETOACETYL-COA THIOLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,83814
Polymers161,1924
Non-polymers3,64710
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19200 Å2
ΔGint-112 kcal/mol
Surface area48200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.459, 78.864, 149.745
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.00123, -0.00039), (-0.00123, -1, 0.00048), (-0.00039, 0.00048, 1)42.23032, 0.01166, 0.03425
2given(0.44082, -0.89683, -0.0372), (-0.89746, -0.4411, -0.00065), (-0.01583, 0.03367, -0.99931)13.46427, 19.38684, 68.78861
3given(-0.43795, 0.89801, -0.0423), (0.89885, 0.43826, -0.002), (0.01674, -0.0389, -0.9991)32.14719, -18.56064, 68.12791

-
Components

#1: Protein
PROTEIN (ACETOACETYL-COA THIOLASE) / BIOSYNTHETIC THIOLASE


Mass: 40297.949 Da / Num. of mol.: 4 / Fragment: RESIDUES 4-392
Source method: isolated from a genetically manipulated source
Details: CYS89 IS ACETYLATED / Source: (gene. exp.) Zoogloea ramigera (bacteria) / Plasmid: PZTH, BASED ON PTRC99A (PHARMACIA) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P07097, acetyl-CoA C-acetyltransferase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Description: ADDITIONAL DATA WERE COLLECTED AT THE ESRF ID14 BEAMLINE IN FEB-1999.
Crystal growpH: 5
Details: 1 M LITHIUM SULPHATE, 0.9 M AMMONIUM SULPHATE, 0.1 M SODIUM ACETATE PH 5.0 A REACTION INTERMEDIATE WAS TRAPPED BY FLASH-FREEZING THE CRYSTAL AFTER A SHORT SOAK WITH ACETOACETYL-COA SUBSTRATE.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
25 mMacetoacetyl-CoA1drop
31 Mlithium sulfate1reservoir
40.9 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH5.0
61 mMdithiothreitol1reservoir
71 mMEDTA1reservoir
81 mMsodium azide1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.2
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 1, 1998 / Details: TOROIDAL MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 130872 / % possible obs: 93 % / Redundancy: 4.4 % / Biso Wilson estimate: 24.19 Å2 / Rsym value: 8.4 / Net I/σ(I): 7
Reflection shellResolution: 2.03→2.15 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 5 / Rsym value: 13 / % possible all: 77

-
Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
XDSV. 1999data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AFW

1afw


Resolution: 1.92→50 Å / SU B: 4.32859 / SU ML: 0.12482 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17198 / ESU R Free: 0.16273
Details: INITIAL SIMULATED ANNEALING MOLECULAR DYNAMICS REFINEMENT WAS CARRIED OUT WITH CNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 6438 5 %RANDOM
Rwork0.209 ---
obs-127433 85.5 %-
Displacement parametersBiso mean: 39.84 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11264 0 222 718 12204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.018
X-RAY DIFFRACTIONp_angle_d0.0410.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3143
X-RAY DIFFRACTIONp_mcangle_it4.0634
X-RAY DIFFRACTIONp_scbond_it5.8195
X-RAY DIFFRACTIONp_scangle_it6.5956
X-RAY DIFFRACTIONp_plane_restr0.0173
X-RAY DIFFRACTIONp_chiral_restr0.2050.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1970.3
X-RAY DIFFRACTIONp_planar_tor2.63
X-RAY DIFFRACTIONp_staggered_tor18.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor35.520
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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