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- PDB-6j7h: Crystal structure of blue fluorescent protein from metagenomic library -

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Basic information

Entry
Database: PDB / ID: 6j7h
TitleCrystal structure of blue fluorescent protein from metagenomic library
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
Blue fluorescent protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.309 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)107,5304
Polymers107,5304
Non-polymers00
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-49 kcal/mol
Surface area32760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.281, 90.564, 171.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.49 %
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% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39207 / % possible obs: 99.8 % / Redundancy: 6.2 % / Rpim(I) all: 0.088 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1928 / Rpim(I) all: 0.327

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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: 2.309→48.347 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2561 1562 4 %
Rwork0.2048 --
obs0.2068 39065 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.309→48.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7091 0 0 273 7364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067179
X-RAY DIFFRACTIONf_angle_d0.879744
X-RAY DIFFRACTIONf_dihedral_angle_d15.0314318
X-RAY DIFFRACTIONf_chiral_restr0.0571139
X-RAY DIFFRACTIONf_plane_restr0.0071318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3086-2.38310.27671340.19813210X-RAY DIFFRACTION95
2.3831-2.46830.29161410.2033380X-RAY DIFFRACTION100
2.4683-2.56710.27341400.21163375X-RAY DIFFRACTION100
2.5671-2.68390.3011420.21413394X-RAY DIFFRACTION100
2.6839-2.82540.31831410.22433398X-RAY DIFFRACTION99
2.8254-3.00240.31291420.21573393X-RAY DIFFRACTION100
3.0024-3.23420.29741430.22853419X-RAY DIFFRACTION100
3.2342-3.55950.27081420.2163428X-RAY DIFFRACTION100
3.5595-4.07440.21441430.19173420X-RAY DIFFRACTION99
4.0744-5.13240.2051460.18363495X-RAY DIFFRACTION100
5.1324-48.35720.24111480.2023591X-RAY DIFFRACTION98

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