[English] 日本語
Yorodumi
- PDB-9ka8: Structure of the recombinant structure of the subunit of allophyc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ka8
TitleStructure of the recombinant structure of the subunit of allophycocyanin (APC) and the formate dehydrogenase (FDH)
Components
  • Allophycocyanin
  • Formate dehydrogenase
KeywordsPHOTOSYNTHESIS / artificial phtosynthesis / formate dehydrogenase / allophycocyanin
Function / homology
Function and homology information


formate catabolic process / formate dehydrogenase / formate dehydrogenase (NAD+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol
Similarity search - Function
NAD-dependent formate dehydrogenase / D-isomer specific 2-hydroxyacid dehydrogenases signature 2. / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / Formate dehydrogenase / :
Similarity search - Component
Biological speciesCandida boidinii (fungus)
Picosynechococcus sp. PCC 7003 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsDuan, M.P. / Zhang, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32472277 China
National Natural Science Foundation of China (NSFC)32372320 China
CitationJournal: To Be Published
Title: Structure of the recombinant structure of the subunit of allophycocyanin (APC) and the formate dehydrogenase (FDH)
Authors: Duan, M.P. / Zhang, T.
History
DepositionOct 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Formate dehydrogenase
F: Allophycocyanin
A: Formate dehydrogenase
C: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1446
Polymers112,9664
Non-polymers1,1772
Water19,3841076
1
A: Formate dehydrogenase
C: Allophycocyanin
hetero molecules

B: Formate dehydrogenase
F: Allophycocyanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1446
Polymers112,9664
Non-polymers1,1772
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_544-x+y+1/3,-x-1/3,z-1/31
Buried area10760 Å2
ΔGint-70 kcal/mol
Surface area43290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.784, 189.784, 153.879
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein Formate dehydrogenase / FDH / NAD-dependent formate dehydrogenase


Mass: 39311.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida boidinii (fungus) / Gene: FDH, Cboi02_000553900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A1EQY0, formate dehydrogenase
#2: Protein Allophycocyanin


Mass: 17171.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Picosynechococcus sp. PCC 7003 (bacteria)
Gene: AWQ21_08925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B1TQ46
#3: Chemical ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1076 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.72 Å3/Da / Density % sol: 73.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.1 M NaCl, 0.1M Hepes (pH 7.5), 1.6 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.19→29.4 Å / Num. obs: 105397 / % possible obs: 99.67 % / Redundancy: 4.9 % / Biso Wilson estimate: 33.37 Å2 / CC1/2: 0.974 / Net I/σ(I): 3.08
Reflection shellResolution: 2.19→2.25 Å / Num. unique obs: 7153 / CC1/2: 0.974

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→29.4 Å / SU ML: 0.2245 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.7858
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2172 2002 1.9 %
Rwork0.1882 103395 -
obs0.1887 105397 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.44 Å2
Refinement stepCycle: LAST / Resolution: 2.19→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7690 0 86 1076 8852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01057928
X-RAY DIFFRACTIONf_angle_d1.060510757
X-RAY DIFFRACTIONf_chiral_restr0.05961202
X-RAY DIFFRACTIONf_plane_restr0.00921391
X-RAY DIFFRACTIONf_dihedral_angle_d18.39982983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.250.22411330.23177153X-RAY DIFFRACTION96.44
2.25-2.310.25041420.21847387X-RAY DIFFRACTION99.85
2.31-2.380.34321420.22287428X-RAY DIFFRACTION99.84
2.38-2.450.25541470.21927365X-RAY DIFFRACTION99.81
2.45-2.540.2311430.22927398X-RAY DIFFRACTION99.88
2.54-2.640.25211450.21557420X-RAY DIFFRACTION99.89
2.64-2.760.31081450.22567375X-RAY DIFFRACTION99.93
2.76-2.910.25991450.21597429X-RAY DIFFRACTION99.96
2.91-3.090.26191430.22077409X-RAY DIFFRACTION99.97
3.09-3.330.20921420.19877385X-RAY DIFFRACTION100
3.33-3.660.21491480.1817446X-RAY DIFFRACTION100
3.66-4.190.19371400.15967365X-RAY DIFFRACTION100
4.19-5.280.15161480.14477425X-RAY DIFFRACTION100
5.28-29.40.18681390.17547410X-RAY DIFFRACTION99.74

+
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