[English] 日本語
Yorodumi
- PDB-2byz: Structure of E.coli KAS I H298Q mutant in complex with C12 fatty acid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2byz
TitleStructure of E.coli KAS I H298Q mutant in complex with C12 fatty acid
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / ACYLTRANSFERASE / CLAISEN CONDENSATION / FATTY ACID BIOSYNTHESIS / FATTY ACID SYNTHASE / THIOLASE FOLD
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / AMMONIUM ION / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsOlsen, J.G. / von Wettstein-Knowles, P. / Henriksen, A.
Citation
Journal: FEBS J. / Year: 2006
Title: Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.
Authors: von Wettstein-Knowles, P. / Olsen, J.G. / McGuire, K.A. / Henriksen, A.
#1: Journal: Structure / Year: 2001
Title: Structures of Beta-Ketoacyl-Acyl Carrier Protein Synthase I Complexed with Fatty Acids Elucidate its Catalytic Machinery
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Lindquist, Y. / Larsen, S.
#2: Journal: Biochemistry / Year: 2001
Title: Beta-Ketoacyl-(Acyl Carrier Protein) Synthase I of Escherichia Coli: Aspects of the Condensation Mechanism Revealed by Analyses of Mutations in the Active Site Pocket
Authors: Mcguire, K.A. / Siggaard-Andersen, M. / Bangera, M.G. / Olsen, J.G. / von Wettstein-Knowles, P.
#3: Journal: FEBS Lett. / Year: 1999
Title: The X-Ray Crystal Structure of Beta-Ketoacyl (Acyl Carrier Protein) Synthase I
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Lindquist, Y. / Larsen, S.
History
DepositionAug 9, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,08012
Polymers176,2074
Non-polymers8738
Water18,2491013
1
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5406
Polymers88,1032
Non-polymers4374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-48.1 kcal/mol
Surface area30480 Å2
MethodPQS
2
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5406
Polymers88,1032
Non-polymers4374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-39.4 kcal/mol
Surface area30760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.100, 139.250, 212.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I / BETA-KETOACYL-ACP SYNTHASE I / KAS I


Mass: 44051.703 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIOESTER LINK FROM C163 TO FATTY ACID LIGAND / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP4)
References: UniProt: P14926, UniProt: P0A953*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#3: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1013 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL HIS-TAG MRGSHHHHHHGS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.46 %
Crystal growpH: 6.8
Details: 1.9 M (NH4)2SO4, 2 % PEG400, 0.1 M BISTRIS-PROPANE PH 6.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.086
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.086 Å / Relative weight: 1
ReflectionResolution: 1.95→212.1 Å / Num. obs: 113763 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.8 / % possible all: 80.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK4

1ek4


Resolution: 1.95→116.4 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3672733.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.217 6140 5 %RANDOM
Rwork0.189 ---
obs0.189 121622 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.9161 Å2 / ksol: 0.382637 e/Å3
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--3.09 Å20 Å2
3----2.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.95→116.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11888 0 56 1013 12957
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.112.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.255 846 5 %
Rwork0.209 16189 -
obs--80.6 %

+
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