[English] 日本語
Yorodumi
- PDB-1f7t: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1f7t
TitleHOLO-(ACYL CARRIER PROTEIN) SYNTHASE AT 1.8A
ComponentsHOLO-(ACYL CARRIER PROTEIN) SYNTHASE
KeywordsTRANSFERASE / 9-strand pseudo beta barrel / LIPID SYNTHESIS
Function / homology
Function and homology information


holo-[acyl-carrier-protein] synthase / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
: / 4'-phosphopantetheinyl transferase domain / Holo-[acyl carrier protein] synthase / Phosphopantetheine-protein transferase domain / 4'-phosphopantetheinyl transferase domain / 4'-phosphopantetheinyl transferase domain superfamily / 4'-phosphopantetheinyl transferase superfamily / Ribosomal Protein L22; Chain A / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Holo-[acyl-carrier-protein] synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsParris, K.D. / Lin, L. / Tam, A. / Mathew, R. / Hixon, J. / Stahl, M. / Fritz, C.C. / Seehra, J. / Somers, W.S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structures of substrate binding to Bacillus subtilis holo-(acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites.
Authors: Parris, K.D. / Lin, L. / Tam, A. / Mathew, R. / Hixon, J. / Stahl, M. / Fritz, C.C. / Seehra, J. / Somers, W.S.
History
DepositionJun 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96340
Polymers82,1506
Non-polymers1,81334
Water8,449469
1
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98122
Polymers41,0753
Non-polymers90619
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7470 Å2
ΔGint-191 kcal/mol
Surface area16070 Å2
MethodPISA
2
D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,98218
Polymers41,0753
Non-polymers90715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-168 kcal/mol
Surface area16080 Å2
MethodPISA
3
A: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
B: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
C: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules

D: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
E: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
F: HOLO-(ACYL CARRIER PROTEIN) SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,96340
Polymers82,1506
Non-polymers1,81334
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area16460 Å2
ΔGint-368 kcal/mol
Surface area30570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.262, 76.160, 85.693
Angle α, β, γ (deg.)90.00, 93.32, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a trimer. The asymmetric unit in this structure contains two such trimers, one constructed from chains A, B, and C. The second from chains D, E. F.

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
HOLO-(ACYL CARRIER PROTEIN) SYNTHASE


Mass: 13691.680 Da / Num. of mol.: 6 / Mutation: Q96P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: PBAD-HIS / Production host: Escherichia coli (E. coli)
References: UniProt: P96618, holo-[acyl-carrier-protein] synthase

-
Non-polymers , 5 types, 503 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein: 10mM Sodium Acetate pH 4.4, 2mM Magnesium chloride, 100mM sodium chloride, 5mM Dithiothreitol Well: 2.5M Sodium chloride, 0.1M Tris pH 7.0, 0.2M Magnesium chloride, VAPOR DIFFUSION, ...Details: Protein: 10mM Sodium Acetate pH 4.4, 2mM Magnesium chloride, 100mM sodium chloride, 5mM Dithiothreitol Well: 2.5M Sodium chloride, 0.1M Tris pH 7.0, 0.2M Magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.5 M11NaCl
20.1 MTris11
30.2 M11MgCl2

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.211.2
SYNCHROTRONNSLS X12C20.978
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMay 30, 1999
BRANDEIS2CCDJul 27, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.21
20.9781
ReflectionResolution: 1.8→20 Å / Num. all: 87902 / Num. obs: 314385 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.76 / Net I/σ(I): 15.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.461 / Num. unique all: 3103 / % possible all: 68.6
Reflection
*PLUS
Num. obs: 87902 / Num. measured all: 314385
Reflection shell
*PLUS
% possible obs: 68.6 % / Mean I/σ(I) obs: 1.9

-
Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 4301 5 %Random
Rwork0.196 ---
all0.197 90806 --
obs0.197 85222 93.9 %-
Solvent computationSolvent model: CNS / Bsol: 57.718 Å2 / ksol: 0.393 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 79 469 6141
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 50 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

+
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