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- PDB-6j7u: Crystal structure of blue fluorescent protein from metagenomic li... -

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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) / 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) 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

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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
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

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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: 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

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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: 2.08 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

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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

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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: 2.302→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

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