[English] 日本語
Yorodumi
- PDB-6j7u: Crystal structure of blue fluorescent protein from metagenomic li... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6j7u
TitleCrystal structure of blue fluorescent protein from metagenomic library in complex with NADPH
ComponentsBlue fluorescent protein
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / BFP
Function / homology
Function and homology information


3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) / branched-chain 2-oxo acid dehydrogenase activity / nucleotide binding
Similarity search - Function
PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Blue fluorescent protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsSeo, P.W. / Kim, J.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea) Korea, Republic Of
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Structure-Guided Generation of a Redox-Independent Blue Fluorescent Protein from mBFP.
Authors: Seo, P.W. / Jo, E.S. / You, S.H. / Cheong, D.E. / Kim, G.J. / Kim, J.S.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Blue fluorescent protein
B: Blue fluorescent protein
C: Blue fluorescent protein
D: Blue fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5118
Polymers107,5304
Non-polymers2,9824
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18440 Å2
ΔGint-62 kcal/mol
Surface area30750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.662, 96.792, 168.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
Blue fluorescent protein


Mass: 26882.391 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: D6NKF4, 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.08 Å3/Da / Density % sol: 40.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M BICINE pH 9.0, 0.3M Magnesium nitrate, 22% w/v PEG 2000, 4% v/v MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 40297 / % possible obs: 99.5 % / Redundancy: 7.4 % / Rpim(I) all: 0.07 / Net I/σ(I): 8.5
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1987 / Rpim(I) all: 0.296

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V2G

3v2g


Resolution: 2.302→19.777 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81
RfactorNum. reflection% reflection
Rfree0.2565 1606 4 %
Rwork0.2042 --
obs0.2064 40139 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.302→19.777 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 0 192 231 7523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147396
X-RAY DIFFRACTIONf_angle_d1.34210076
X-RAY DIFFRACTIONf_dihedral_angle_d16.7074364
X-RAY DIFFRACTIONf_chiral_restr0.0811172
X-RAY DIFFRACTIONf_plane_restr0.0091340
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3024-2.37660.35241440.26553427X-RAY DIFFRACTION98
2.3766-2.46140.34771410.25593437X-RAY DIFFRACTION100
2.4614-2.55970.30641440.24413475X-RAY DIFFRACTION99
2.5597-2.6760.3091440.22663449X-RAY DIFFRACTION99
2.676-2.81670.2911470.22573486X-RAY DIFFRACTION100
2.8167-2.99260.26891440.22183495X-RAY DIFFRACTION100
2.9926-3.22270.28871470.22093515X-RAY DIFFRACTION99
3.2227-3.54540.2421460.20153507X-RAY DIFFRACTION100
3.5454-4.05450.23281470.17923535X-RAY DIFFRACTION99
4.0545-5.09380.21411490.16393553X-RAY DIFFRACTION99
5.0938-19.7770.20181530.18783654X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.3715 Å / Origin y: 0.0367 Å / Origin z: -19.5246 Å
111213212223313233
T0.1651 Å20.0035 Å2-0.0008 Å2-0.2143 Å20.016 Å2--0.2166 Å2
L0.2388 °20.0107 °2-0.0562 °2-0.5607 °20.0398 °2--0.9259 °2
S0.0163 Å °0.0215 Å °-0.0026 Å °0.0238 Å °-0.0188 Å °0.0046 Å °0.0765 Å °-0.0227 Å °0.0004 Å °
Refinement TLS groupSelection details: all

+
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