[English] 日本語
Yorodumi
- PDB-5hz2: Crystal structure of PhaC1 from Ralstonia eutropha -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hz2
TitleCrystal structure of PhaC1 from Ralstonia eutropha
ComponentsPoly-beta-hydroxybutyrate polymerase
KeywordsTRANSFERASE
Function / homology
Function and homology information


poly-hydroxybutyrate biosynthetic process / acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function
Poly-beta-hydroxybutyrate polymerase, N-terminal domain / Poly(R)-hydroxyalkanoic acid synthase, class I / Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Poly(3-hydroxyalkanoate) polymerase subunit PhaC
Similarity search - Component
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / SIR / Resolution: 1.8 Å
AuthorsKim, J. / Kim, K.-J.
CitationJournal: Biotechnol J / Year: 2017
Title: Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms.
Authors: Kim, J. / Kim, Y.J. / Choi, S.Y. / Lee, S.Y. / Kim, K.J.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly-beta-hydroxybutyrate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,50710
Polymers43,6501
Non-polymers8579
Water5,044280
1
A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules

A: Poly-beta-hydroxybutyrate polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,02840
Polymers174,6024
Non-polymers3,42736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area26870 Å2
ΔGint-522 kcal/mol
Surface area49070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.246, 87.856, 136.479
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Poly-beta-hydroxybutyrate polymerase / PHB polymerase / PHB synthase / Poly(3-hydroxyalkanoate) polymerase / PHA polymerase / Poly(3- ...PHB polymerase / PHB synthase / Poly(3-hydroxyalkanoate) polymerase / PHA polymerase / Poly(3-hydroxybutyrate) polymerase / Polyhydroxyalkanoate synthase / PHA synthase


Mass: 43650.387 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP RESIDUES 202-589)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Strain: ATCC 17699 / H16 / DSM 428 / Stanier 337 / Gene: phbC, H16_A1437 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P23608, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate, HEPES

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 7A (6B, 6C1)10.9798
SYNCHROTRONPAL/PLS 7A (6B, 6C1)21.0072
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2701CCDSep 15, 2013Rh coated Torroidal Mirror
ADSC QUANTUM 2702CCDOct 16, 2013Rh coated Torroidal Mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
21.00721
ReflectionResolution: 1.8→50 Å / Num. obs: 40301 / % possible obs: 98.1 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.054 / Net I/av σ(I): 52.17 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.835.10.261193.5
1.83-1.865.60.245194.9
1.86-1.960.217195.2
1.9-1.946.70.194195.6
1.94-1.987.30.171196.8
1.98-2.037.80.158197.6
2.03-2.088.30.135198.3
2.08-2.138.70.122198.4
2.13-2.29.30.109198.5
2.2-2.279.80.099198.7
2.27-2.3510.10.087198.7
2.35-2.4410.60.081199
2.44-2.5511.10.071199.5
2.55-2.6911.60.068199.5
2.69-2.8611.80.061199.7
2.86-3.0812.50.057199.4
3.08-3.3912.90.051199.6
3.39-3.8813.30.046199.8
3.88-4.8813.40.043199.7
4.88-5012.40.045199.1

-
Phasing

PhasingMethod: SIR
Phasing dmFOM : 0.68 / FOM acentric: 0.69 / FOM centric: 0.57 / Reflection: 29169 / Reflection acentric: 26571 / Reflection centric: 2598

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVE2.15model building
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.477 / SU ML: 0.075 / SU R Cruickshank DPI: 0.1023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1896 2001 5 %RANDOM
Rwork0.1515 ---
obs0.1534 38300 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.91 Å2 / Biso mean: 30.381 Å2 / Biso min: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-0 Å2
2---0.83 Å20 Å2
3----0.37 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 47 280 3340
Biso mean--56.38 37.88 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193142
X-RAY DIFFRACTIONr_bond_other_d0.0020.022919
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.954306
X-RAY DIFFRACTIONr_angle_other_deg1.19636686
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2075387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99423.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37815448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6521518
X-RAY DIFFRACTIONr_chiral_restr0.1920.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02742
X-RAY DIFFRACTIONr_mcbond_it2.6112.7661551
X-RAY DIFFRACTIONr_mcbond_other2.62.7651550
X-RAY DIFFRACTIONr_mcangle_it3.5594.1351937
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 130 -
Rwork0.248 2688 -
all-2818 -
obs--93.34 %

+
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://pdbjlvh1.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