[English] 日本語
Yorodumi
- PDB-9knj: Crystal structure of glycerol-bound full-length PHA synthase (Pha... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9knj
TitleCrystal structure of glycerol-bound full-length PHA synthase (PhaC) from Aeromonas caviae
ComponentsPHA synthase
KeywordsBIOSYNTHETIC PROTEIN / PHA synthase / full-length PhaC structure / dimer / tunnel / catalytic triad / glycerol / polyhydroxyalkanoate
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 / PHA synthase
Function and homology information
Biological speciesAeromonas caviae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChek, M.F. / Kim, S.Y. / Mori, T. / Hakoshima, T.
Funding support Japan, 3items
OrganizationGrant numberCountry
New Energy and Industrial Technology Development Organization (NEDO)P20005 Japan
Japan Science and Technology29A1027 Japan
Japan Society for the Promotion of Science (JSPS)21K5028 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Structures of Polyhydroxyalkanoate Synthase PhaC from Aeromonas caviae, Producing Biodegradable Plastics.
Authors: Chek, M.F. / Kim, S.Y. / Mori, T. / Matsumoto, K. / Sato, S. / Hakoshima, T.
History
DepositionNov 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PHA synthase
B: PHA synthase
C: PHA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,67614
Polymers199,6633
Non-polymers1,01311
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Monomer-dimer equilibrium, gel filtration, Monomer-dimer equilibrium
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.032, 96.071, 143.296
Angle α, β, γ (deg.)90.000, 90.420, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 40 or resid 53...
d_2ens_1(chain "B" and (resid 5 through 77 or resid 105...
d_3ens_1(chain "C" and (resid 5 through 40 or resid 53...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERLEULEUAA5 - 407 - 42
d_12GLNGLNLEULEUAA53 - 7755 - 79
d_13GLNGLNLEULEUAA105 - 166107 - 168
d_14ASPASPASNASNAA171 - 194173 - 196
d_15PHEPHEARGARGAA203 - 553205 - 555
d_16GLUGLUPROPROAA558 - 583560 - 585
d_17GOLGOLGOLGOLAF603
d_21SERSERLEULEUBB5 - 777 - 79
d_22GLNGLNLEULEUBB105 - 166107 - 168
d_23ASPASPASNASNBB171 - 194173 - 196
d_24PHEPHEARGARGBB203 - 553205 - 555
d_25GLUGLUPROPROBB558 - 583560 - 585
d_26GOLGOLGOLGOLBK603
d_31SERSERLEULEUCC5 - 407 - 42
d_32GLNGLNLEULEUCC53 - 7755 - 79
d_33GLNGLNASNASNCC105 - 194107 - 196
d_34PHEPHEPROPROCC203 - 583205 - 585
d_35GOLGOLGOLGOLCM601

NCS oper:
IDCodeMatrixVector
1given(0.456425170661, -0.889246047369, -0.0302907712805), (-0.887348698739, -0.452417880868, -0.0890525009047), (0.0654854978853, 0.0675242794028, -0.995566231477)5.95315826582, -76.4060249109, 101.288550773
2given(-0.446619192675, -0.893308726761, 0.050307210492), (0.893787775271, -0.442874282119, 0.0707515583807), (-0.0409232148014, 0.0765629736303, 0.996224573858)-72.0007114008, 52.4370521268, -49.3858026235

-
Components

#1: Protein PHA synthase


Mass: 66554.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas caviae (bacteria) / Gene: phaC / Production host: Escherichia coli (E. coli) / References: UniProt: O32471
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.56 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium chloride, glycerol, PEG6000, octyl beta-D-glucopyranoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.999994 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999994 Å / Relative weight: 1
ReflectionResolution: 2.68→50 Å / Num. obs: 59959 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 71.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.036 / Rrim(I) all: 0.069 / Net I/σ(I): 14.83
Reflection shellResolution: 2.68→2.84 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.574 / Num. unique obs: 9640 / CC1/2: 0.816 / Rrim(I) all: 0.677 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
BUCCANEERmodel building
PHENIX1.20.1_4487model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→48.04 Å / SU ML: 0.4298 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 3808 3.37 %
Rwork0.2101 109092 -
obs0.2115 58604 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.06 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12781 0 66 27 12874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004713127
X-RAY DIFFRACTIONf_angle_d0.761217820
X-RAY DIFFRACTIONf_chiral_restr0.05121963
X-RAY DIFFRACTIONf_plane_restr0.00542298
X-RAY DIFFRACTIONf_dihedral_angle_d16.54784791
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.30018052713
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.71729752873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.38661460.36664028X-RAY DIFFRACTION98.17
2.73-2.770.38471330.34424035X-RAY DIFFRACTION98.98
2.77-2.810.39321480.33724102X-RAY DIFFRACTION98.88
2.81-2.850.34161300.30394028X-RAY DIFFRACTION98.72
2.85-2.890.36661550.28384076X-RAY DIFFRACTION98.76
2.89-2.940.31411200.28494100X-RAY DIFFRACTION98.76
2.94-2.980.32231540.28554101X-RAY DIFFRACTION98.98
2.98-3.040.33961300.27734046X-RAY DIFFRACTION98.65
3.04-3.090.32521510.27954034X-RAY DIFFRACTION98.61
3.09-3.150.31911450.28564058X-RAY DIFFRACTION98.48
3.15-3.210.35261320.28974044X-RAY DIFFRACTION98.4
3.21-3.280.38951520.27544075X-RAY DIFFRACTION98.12
3.28-3.360.32911280.24793955X-RAY DIFFRACTION97.63
3.36-3.440.28071620.23133997X-RAY DIFFRACTION97.06
3.44-3.540.26751240.23434050X-RAY DIFFRACTION97.07
3.54-3.640.26371440.22464001X-RAY DIFFRACTION98.11
3.64-3.760.2371340.22124013X-RAY DIFFRACTION97.71
3.76-3.890.27521210.22174014X-RAY DIFFRACTION97.16
3.89-4.050.24041450.20573932X-RAY DIFFRACTION95.97
4.05-4.230.26971610.18684054X-RAY DIFFRACTION98.37
4.23-4.460.22841530.17864044X-RAY DIFFRACTION98.61
4.46-4.740.17471580.16534045X-RAY DIFFRACTION98.82
4.74-5.10.22991360.17214121X-RAY DIFFRACTION98.77
5.1-5.610.21731220.18644035X-RAY DIFFRACTION98.53
5.61-6.420.18731530.20963997X-RAY DIFFRACTION97.49
6.42-8.090.26971440.18884061X-RAY DIFFRACTION98.57

+
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