[English] 日本語
Yorodumi
- PDB-5xav: Structure of PhaC from Chromobacterium sp. USM2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xav
TitleStructure of PhaC from Chromobacterium sp. USM2
ComponentsIntracellular polyhydroxyalkanoate synthase
KeywordsBIOSYNTHETIC PROTEIN / bioplastic synthase / PhaC
Function / homologyPoly-beta-hydroxybutyrate polymerase, N-terminal domain / Poly(R)-hydroxyalkanoic acid synthase, class I / : / Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus / poly-hydroxybutyrate biosynthetic process / acyltransferase activity / Alpha/Beta hydrolase fold / cytoplasm / Intracellular polyhydroxyalkanoate synthase
Function and homology information
Biological speciesChromobacterium sp. USM2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.479 Å
AuthorsChek, M.F. / Kim, S.Y. / Mori, T. / Arsad, H. / Samian, M.R. / Sudesh, K. / Hakoshima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (MEXT) Japan
CitationJournal: Sci Rep / Year: 2017
Title: Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics
Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Arsad, H. / Samian, M.R. / Sudesh, K. / Hakoshima, T.
History
DepositionMar 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Intracellular polyhydroxyalkanoate synthase
B: Intracellular polyhydroxyalkanoate synthase


Theoretical massNumber of molelcules
Total (without water)87,6592
Polymers87,6592
Non-polymers00
Water18,8981049
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Analytical ultracentrifugation with a sedimentation velocity method
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-11 kcal/mol
Surface area28160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.332, 117.332, 105.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Intracellular polyhydroxyalkanoate synthase


Mass: 43829.395 Da / Num. of mol.: 2 / Fragment: UNP residues 175-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium sp. USM2 (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: E1APK1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 50 mM Bis-Tris pH5.5, 60 mM Ammonium sulfate 5% PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.479→50 Å / Num. obs: 137720 / % possible obs: 99.8 % / Redundancy: 11.2 % / Net I/σ(I): 58.6
Reflection shellResolution: 1.48→1.51 Å / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 6.2

-
Processing

Software
NameVersionClassification
HKL-2000data processing
autoSHARPphasing
BUCCANEERmodel building
REFMACrefinement
Cootrefinement
PHENIX(1.10.1_2155)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.479→36.105 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.17
RfactorNum. reflection% reflection
Rfree0.1574 6908 5.03 %
Rwork0.1211 --
obs0.123 137380 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.479→36.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5919 0 0 1049 6968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0196098
X-RAY DIFFRACTIONf_angle_d1.6038314
X-RAY DIFFRACTIONf_dihedral_angle_d13.8882203
X-RAY DIFFRACTIONf_chiral_restr0.132908
X-RAY DIFFRACTIONf_plane_restr0.0121059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4787-1.49550.2062240.17384260X-RAY DIFFRACTION98
1.4955-1.51310.22912260.16874348X-RAY DIFFRACTION100
1.5131-1.53160.20682310.164346X-RAY DIFFRACTION100
1.5316-1.55090.20222370.14684365X-RAY DIFFRACTION100
1.5509-1.57140.17121900.13764346X-RAY DIFFRACTION100
1.5714-1.59290.18672310.12834393X-RAY DIFFRACTION100
1.5929-1.61560.17992350.12334311X-RAY DIFFRACTION100
1.6156-1.63980.17342500.11824332X-RAY DIFFRACTION100
1.6398-1.66540.19022450.1184335X-RAY DIFFRACTION100
1.6654-1.69270.15212320.11064333X-RAY DIFFRACTION100
1.6927-1.72190.1732370.11244356X-RAY DIFFRACTION100
1.7219-1.75320.16862090.10934376X-RAY DIFFRACTION100
1.7532-1.78690.14812250.10764327X-RAY DIFFRACTION100
1.7869-1.82340.15512620.11344328X-RAY DIFFRACTION100
1.8234-1.8630.1632390.11054391X-RAY DIFFRACTION100
1.863-1.90640.15621980.10824364X-RAY DIFFRACTION100
1.9064-1.9540.14672210.10494366X-RAY DIFFRACTION100
1.954-2.00690.1472340.10424326X-RAY DIFFRACTION100
2.0069-2.06590.16452080.10714391X-RAY DIFFRACTION100
2.0659-2.13260.14822180.1044384X-RAY DIFFRACTION100
2.1326-2.20880.13872120.1054352X-RAY DIFFRACTION100
2.2088-2.29720.15352420.10944370X-RAY DIFFRACTION100
2.2972-2.40170.16592470.11624341X-RAY DIFFRACTION100
2.4017-2.52830.15952250.12014354X-RAY DIFFRACTION100
2.5283-2.68670.16892400.1214378X-RAY DIFFRACTION100
2.6867-2.8940.14362310.1254356X-RAY DIFFRACTION100
2.894-3.18510.16242490.12864383X-RAY DIFFRACTION100
3.1851-3.64560.14832420.12494375X-RAY DIFFRACTION100
3.6456-4.59170.13532360.11794358X-RAY DIFFRACTION100
4.5917-36.11610.16122320.14394227X-RAY DIFFRACTION95

+
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