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- PDB-3p19: Improved NADPH-dependent Blue Fluorescent Protein -

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Basic information

Entry
Database: PDB / ID: 3p19
TitleImproved NADPH-dependent Blue Fluorescent Protein
ComponentsPutative blue fluorescent protein
KeywordsOXIDOREDUCTASE / Rossmann-fold / Blue fluorescent protein
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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 / Putative blue fluorescent protein
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKao, T.H. / Chen, Y. / Pai, C.H. / Wang, A.H.J.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structure of a NADPH-dependent blue fluorescent protein revealed the unique role of Gly176 on the fluorescence enhancement.
Authors: Kao, T.H. / Chen, Y. / Pai, C.H. / Chang, M.C. / Wang, A.H.J.
History
DepositionSep 30, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Non-polymer description
Revision 1.2Nov 1, 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative blue fluorescent protein
B: Putative blue fluorescent protein
C: Putative blue fluorescent protein
D: Putative blue fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5478
Polymers115,5654
Non-polymers2,9824
Water9,782543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-50 kcal/mol
Surface area31430 Å2
MethodPISA
2
A: Putative blue fluorescent protein
B: Putative blue fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2734
Polymers57,7822
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area18350 Å2
MethodPISA
3
C: Putative blue fluorescent protein
D: Putative blue fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2734
Polymers57,7822
Non-polymers1,4912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-18 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.403, 64.403, 262.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Putative blue fluorescent protein / BFPvvD8


Mass: 28891.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9F172*PLUS
#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.: 543 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M sodium citrate dihydrate, 0.1M HEPES-Na, 20% iso-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2008
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 66791 / Num. obs: 66383 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.293 / Num. unique all: 6413 / % possible all: 96.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JAP

2jap


Resolution: 2.05→24.32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.055 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 3352 5.1 %RANDOM
Rwork0.1863 ---
all0.189 66383 --
obs0.189 66194 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.86 Å2 / Biso mean: 35.538 Å2 / Biso min: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 192 543 7647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227216
X-RAY DIFFRACTIONr_angle_refined_deg1.2741.9989818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6495907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.65924.452292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.771151219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.861550
X-RAY DIFFRACTIONr_chiral_restr0.1080.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215282
X-RAY DIFFRACTIONr_mcbond_it1.51.54535
X-RAY DIFFRACTIONr_mcangle_it2.48127284
X-RAY DIFFRACTIONr_scbond_it4.06232681
X-RAY DIFFRACTIONr_scangle_it6.054.52534
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 238 -
Rwork0.313 4431 -
all-4669 -
obs--95.5 %

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