[English] 日本語
Yorodumi
- PDB-6olt: Crosslinked Crystal Structure of Type II Fatty Acid Synthase Keto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6olt
TitleCrosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and C12-crypto Acyl Carrier Protein, AcpP
Components
  • 3-oxoacyl-[acyl-carrier-protein] synthase 2
  • Acyl carrier protein
KeywordsTRANSFERASE / ketosynthase / KS / AcpP / beta-ketoacyl-Acyl carrier protein synthase / beta-ketoacyl-ACP synthase / acyl carrier protein / TRANSFERASE-TRANSPORT PROTEIN complex
Function / homology
Function and homology information


fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl binding / acyl carrier activity / response to cold ...fatty acid elongation, saturated fatty acid / monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase II / lipid biosynthetic process / lipid A biosynthetic process / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / acyl binding / acyl carrier activity / response to cold / fatty acid biosynthetic process / response to xenobiotic stimulus / lipid binding / protein homodimerization activity / cytosol / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / 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 / Acyl carrier protein (ACP) / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MRJ / Acyl carrier protein / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsMindrebo, J.T. / Kim, W.E. / Bartholow, T.G. / Chen, A. / Davis, T.D. / La Clair, J. / Burkart, M.D. / Noel, J.P.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM095970-06 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2020
Title: Gating mechanism of elongating beta-ketoacyl-ACP synthases.
Authors: Mindrebo, J.T. / Patel, A. / Kim, W.E. / Davis, T.D. / Chen, A. / Bartholow, T.G. / La Clair, J.J. / McCammon, J.A. / Noel, J.P. / Burkart, M.D.
History
DepositionApr 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2593
Polymers51,7352
Non-polymers5241
Water1,65792
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: Acyl carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5176
Polymers103,4704
Non-polymers1,0472
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area9270 Å2
ΔGint-57 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.450, 86.450, 115.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21A-631-

HOH

31A-686-

HOH

-
Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2 / 3-oxoacyl-[acyl-carrier-protein] synthase II / Beta-ketoacyl-ACP synthase II / KAS II


Mass: 43089.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fabF, fabJ, b1095, JW1081 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0AAI5, beta-ketoacyl-[acyl-carrier-protein] synthase II
#2: Protein Acyl carrier protein / ACP / Cytosolic-activating factor / CAF / Fatty acid synthase acyl carrier protein


Mass: 8645.460 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: acpP, b1094, JW1080 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6A8
#3: Chemical ChemComp-MRJ / N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide


Mass: 523.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N3O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.87 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 % PEG 8K, 0.1 M sodium cacodylate pH 6.5, and 0.3 M sodium acetate
Temp details: 279

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→86.45 Å / Num. obs: 18833 / % possible obs: 99.9 % / Redundancy: 15.3 % / Biso Wilson estimate: 40.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.086 / Rrim(I) all: 0.342 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.35-2.4315.94.09817980.4481.0494.23299.8
9.1-86.4512.90.044050.9990.0120.042100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GFW was used as the search model for FabF, 2FAC was used as the search model for AcpP

2gfw

2fac


Resolution: 2.35→69.137 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.84
RfactorNum. reflection% reflection
Rfree0.2389 1075 5.73 %
Rwork0.2006 --
obs0.2029 18770 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.33 Å2 / Biso mean: 58.9403 Å2 / Biso min: 21.73 Å2
Refinement stepCycle: final / Resolution: 2.35→69.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 48 92 3748
Biso mean--58.36 46.56 -
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.35-2.4570.31611220.31321702292
2.457-2.58650.39271270.296321682295
2.5865-2.74860.35071350.280321562291
2.7486-2.96080.30641240.259421882312
2.9608-3.25880.22861400.223421832323
3.2588-3.73030.25151380.187922192357
3.7303-4.69970.18891410.142422362377
4.6997-69.16670.19091480.173323752523
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)
12.62610.11160.43051.11880.19692.6321-0.0168-0.2523-0.01750.37260.02690.18440.6612-0.11080.04260.4837-0.01090.030.3153-0.00760.2754-6.8894-3.934-10.865
21.4525-0.69270.53792.5445-0.10813.84310.02230.02920.13560.2505-0.0838-0.11440.1150.3950.09670.20250.0321-0.00310.2843-0.0250.30632.02144.9248-17.9955
32.5159-0.10890.19571.09280.38113.20220.216-0.0982-0.39330.2311-0.01570.00540.83060.2048-0.13970.47540.1041-0.05280.20.01570.3322-1.4242-8.763-19.7487
40.7457-0.6949-0.81322.8272-1.12492.47850.2840.2082-0.2963-0.1132-0.00840.40521.55360.2246-0.36040.80270.1619-0.12150.3303-0.04230.5148-2.3493-19.7988-30.1943
51.8055-1.31390.09061.3985-0.37790.24460.26780.2861-0.60640.1417-0.1570.29921.5188-0.1726-0.14871.1589-0.0446-0.08660.30.01080.5682-7.1065-23.2933-20.3408
62.3708-0.7748-2.46942.575-0.25233.1543-0.1184-0.048-0.56440.19340.13840.26181.5758-0.394-0.02121.1539-0.1148-0.13070.39080.00470.5354-8.4229-24.3416-18.9279
78.99-3.3173-3.70328.13094.70794.85860.71271.16480.7221-1.0966-0.14240.0281-1.4636-1.302-0.52020.81490.0623-0.04140.89140.22320.4265-27.25362.2842-53.7148
88.3878-4.06730.42195.7108-3.08144.9279-0.08791.8901-1.7099-0.54880.36230.80831.9654-0.8831-0.44021.0405-0.3615-0.11920.8605-0.13010.6325-28.2831-8.9729-52.844
92.46651.82491.71147.133.98912.91740.12150.07310.2182-0.28840.4236-0.5431-0.5025-0.6805-0.6650.54380.0249-0.04610.48650.00160.554-24.7172-1.1909-43.2518
106.28161.9067-2.41034.6736-4.75314.9044-0.0893-0.1478-0.18462.3207-1.2844-0.1133-1.6585-0.24361.56680.7537-0.11870.00961.1261-0.00690.4669-33.47334.8701-36.5382
116.32191.07155.45688.5455-0.51564.96560.2467-1.5948-0.25531.51530.09620.64230.345-1.5215-0.37320.996-0.49510.04951.44640.22650.857-33.1314-6.7035-38.7933
123.8442.22181.61381.8815-1.33259.28380.4981-2.49460.19210.5992-0.25750.7064-0.4596-2.8894-0.02370.6921-0.0585-0.1242.3557-0.10470.8239-37.80370.9372-45.704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 71 )A1 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 138 )A72 - 138
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 249 )A139 - 249
4X-RAY DIFFRACTION4chain 'A' and (resid 250 through 290 )A250 - 290
5X-RAY DIFFRACTION5chain 'A' and (resid 291 through 359 )A291 - 359
6X-RAY DIFFRACTION6chain 'A' and (resid 360 through 412 )A360 - 412
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )B1 - 20
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 30 )B21 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 50 )B31 - 50
10X-RAY DIFFRACTION10chain 'B' and (resid 51 through 55 )B51 - 55
11X-RAY DIFFRACTION11chain 'B' and (resid 56 through 64 )B56 - 64
12X-RAY DIFFRACTION12chain 'B' and (resid 65 through 77 )B65 - 77

+
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