[English] 日本語
Yorodumi
- PDB-5mg5: A multi-component acyltransferase PhlABC from Pseudomonas protege... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mg5
TitleA multi-component acyltransferase PhlABC from Pseudomonas protegens soaked with the monoacetylphloroglucinol (MAPG)
Components
  • (2,4-diacetylphloroglucinol biosynthesis ...) x 2
  • Hydroxymethylglutaryl-CoA synthase
KeywordsTRANSFERASE / acyltransferase / Pseudomonas protegens / PhlABC / multi-component / MAPG
Function / homology
Function and homology information


acetyl-CoA C-acyltransferase activity
Similarity search - Function
: / Thiolase C-terminal domain-like / Thiolase / Thiolase, N-terminal / Thiolase, N-terminal domain / Thiolase-like
Similarity search - Domain/homology
benzene-1,3,5-triol / : / : / 2,4-diacetylphloroglucinol biosynthesis protein PhlC
Similarity search - Component
Biological speciesPseudomonas protegens (bacteria)
Pseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsPavkov-Keller, T. / Schmidt, N.G. / Kroutil, W. / Gruber, K.
CitationJournal: Chembiochem / Year: 2019
Title: Structure and Catalytic Mechanism of a Bacterial Friedel-Crafts Acylase.
Authors: Pavkov-Keller, T. / Schmidt, N.G. / Zadlo-Dobrowolska, A. / Kroutil, W. / Gruber, K.
History
DepositionNov 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 27, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 17, 2024Group: 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 / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hydroxymethylglutaryl-CoA synthase
B: 2,4-diacetylphloroglucinol biosynthesis protein
C: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
D: Hydroxymethylglutaryl-CoA synthase
E: 2,4-diacetylphloroglucinol biosynthesis protein
F: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
G: Hydroxymethylglutaryl-CoA synthase
H: 2,4-diacetylphloroglucinol biosynthesis protein
I: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
J: Hydroxymethylglutaryl-CoA synthase
K: 2,4-diacetylphloroglucinol biosynthesis protein
L: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
M: Hydroxymethylglutaryl-CoA synthase
N: 2,4-diacetylphloroglucinol biosynthesis protein
O: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
P: Hydroxymethylglutaryl-CoA synthase
Q: 2,4-diacetylphloroglucinol biosynthesis protein
R: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
S: Hydroxymethylglutaryl-CoA synthase
T: 2,4-diacetylphloroglucinol biosynthesis protein
U: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
V: Hydroxymethylglutaryl-CoA synthase
W: 2,4-diacetylphloroglucinol biosynthesis protein
X: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)783,53936
Polymers782,51124
Non-polymers1,02812
Water1,11762
1
A: Hydroxymethylglutaryl-CoA synthase
B: 2,4-diacetylphloroglucinol biosynthesis protein
C: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
D: Hydroxymethylglutaryl-CoA synthase
E: 2,4-diacetylphloroglucinol biosynthesis protein
F: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
J: Hydroxymethylglutaryl-CoA synthase
K: 2,4-diacetylphloroglucinol biosynthesis protein
L: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
M: Hydroxymethylglutaryl-CoA synthase
N: 2,4-diacetylphloroglucinol biosynthesis protein
O: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,89519
Polymers391,25512
Non-polymers6407
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69300 Å2
ΔGint-321 kcal/mol
Surface area93080 Å2
MethodPISA
2
G: Hydroxymethylglutaryl-CoA synthase
H: 2,4-diacetylphloroglucinol biosynthesis protein
I: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
P: Hydroxymethylglutaryl-CoA synthase
Q: 2,4-diacetylphloroglucinol biosynthesis protein
R: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
S: Hydroxymethylglutaryl-CoA synthase
T: 2,4-diacetylphloroglucinol biosynthesis protein
U: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
V: Hydroxymethylglutaryl-CoA synthase
W: 2,4-diacetylphloroglucinol biosynthesis protein
X: 2,4-diacetylphloroglucinol biosynthesis protein PhlC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,64317
Polymers391,25512
Non-polymers3885
Water19811
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69500 Å2
ΔGint-357 kcal/mol
Surface area93190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.793, 229.775, 311.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 8 molecules ADGJMPSV

#1: Protein
Hydroxymethylglutaryl-CoA synthase


Mass: 38565.480 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Gene: CEP86_09500 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z3SPL2

-
2,4-diacetylphloroglucinol biosynthesis ... , 2 types, 16 molecules BEHKNQTWCFILORUX

#2: Protein
2,4-diacetylphloroglucinol biosynthesis protein


Mass: 16666.434 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas protegens (bacteria) / Gene: CEP86_09490 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Z3SPP2
#3: Protein
2,4-diacetylphloroglucinol biosynthesis protein PhlC


Mass: 42581.941 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (bacteria)
Strain: ATCC BAA-477 / NRRL B-23932 / Pf-5 / Gene: phlC, PFL_5955 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4K420

-
Non-polymers , 3 types, 74 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Zn
#5: Chemical
ChemComp-13X / benzene-1,3,5-triol / Phloroglucinol


Mass: 126.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Index screen #55 (0.05 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 0% v/v Polyethylene glycol monomethyl ether 550). 12mg/ml in potassium phosphate buffer, 50 mM, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.95 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.44→49.72 Å / Num. obs: 99724 / % possible obs: 99 % / Redundancy: 6 % / CC1/2: 0.97 / Rmerge(I) obs: 0.268 / Net I/σ(I): 8.1
Reflection shellResolution: 3.44→3.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.57 / CC1/2: 0.81 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M3K

5m3k


Resolution: 3.44→49.725 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2206 4986 5 %
Rwork0.1654 --
obs0.1682 99696 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.44→49.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms54406 0 44 62 54512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00455530
X-RAY DIFFRACTIONf_angle_d0.55575132
X-RAY DIFFRACTIONf_dihedral_angle_d7.31233665
X-RAY DIFFRACTIONf_chiral_restr0.0428315
X-RAY DIFFRACTIONf_plane_restr0.0049849
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4401-3.47910.33611290.25372467X-RAY DIFFRACTION78
3.4791-3.52010.27571650.22513133X-RAY DIFFRACTION100
3.5201-3.5630.29261660.21763138X-RAY DIFFRACTION100
3.563-3.60810.29881670.20153190X-RAY DIFFRACTION100
3.6081-3.65550.28071640.19293107X-RAY DIFFRACTION100
3.6555-3.70560.25031660.19043162X-RAY DIFFRACTION100
3.7056-3.75850.26591660.19353137X-RAY DIFFRACTION100
3.7585-3.81460.2561650.18893135X-RAY DIFFRACTION100
3.8146-3.87420.25551660.18283155X-RAY DIFFRACTION100
3.8742-3.93770.22971650.18193147X-RAY DIFFRACTION100
3.9377-4.00550.23211670.17083160X-RAY DIFFRACTION100
4.0055-4.07830.21071650.16883134X-RAY DIFFRACTION100
4.0783-4.15680.19831660.15063153X-RAY DIFFRACTION100
4.1568-4.24160.19751660.14983162X-RAY DIFFRACTION100
4.2416-4.33370.19421670.14453175X-RAY DIFFRACTION100
4.3337-4.43450.20011660.14523151X-RAY DIFFRACTION100
4.4345-4.54530.19151660.14373149X-RAY DIFFRACTION100
4.5453-4.66810.19641670.14283174X-RAY DIFFRACTION100
4.6681-4.80540.2091670.14733176X-RAY DIFFRACTION100
4.8054-4.96030.22421670.15223181X-RAY DIFFRACTION100
4.9603-5.13750.22771670.15373167X-RAY DIFFRACTION100
5.1375-5.34290.19591680.15943197X-RAY DIFFRACTION100
5.3429-5.58580.20121670.15943171X-RAY DIFFRACTION100
5.5858-5.87980.2161700.16693226X-RAY DIFFRACTION100
5.8798-6.24760.22391670.16783174X-RAY DIFFRACTION100
6.2476-6.72890.26661690.17583201X-RAY DIFFRACTION100
6.7289-7.4040.17061710.14763249X-RAY DIFFRACTION100
7.404-8.47090.16491700.13163241X-RAY DIFFRACTION100
8.4709-10.65510.17731730.12873284X-RAY DIFFRACTION100
10.6551-49.72980.22651810.18953414X-RAY DIFFRACTION99

+
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