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- PDB-6lof: Crystal structure of ZsYellow soaked by Cu2+ -

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Basic information

Entry
Database: PDB / ID: 6lof
TitleCrystal structure of ZsYellow soaked by Cu2+
Components(GFP-like fluorescent chromoprotein FP538) x 2
KeywordsFLUORESCENT PROTEIN / ZsYellow / yellow
Function / homology
Function and homology information


Pantoate--beta-alanine Ligase; Chain: A,domain 2 - #40 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GFP-like fluorescent chromoprotein FP538
Similarity search - Component
Biological speciesZoanthus sp. (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNam, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017R1D1A1B03033087 Korea, Republic Of
CitationJournal: Biosensors (Basel) / Year: 2020
Title: Spectroscopic and Structural Analysis of Cu 2+ -Induced Fluorescence Quenching of ZsYellow.
Authors: Kim, I.J. / Xu, Y. / Nam, K.H.
History
DepositionJan 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 14, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
C: GFP-like fluorescent chromoprotein FP538
A: GFP-like fluorescent chromoprotein FP538
D: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538


Theoretical massNumber of molelcules
Total (without water)52,8694
Polymers52,8694
Non-polymers00
Water97354
1
C: GFP-like fluorescent chromoprotein FP538
A: GFP-like fluorescent chromoprotein FP538
D: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538

C: GFP-like fluorescent chromoprotein FP538
A: GFP-like fluorescent chromoprotein FP538
D: GFP-like fluorescent chromoprotein FP538
B: GFP-like fluorescent chromoprotein FP538


Theoretical massNumber of molelcules
Total (without water)105,7388
Polymers105,7388
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area27520 Å2
ΔGint-145 kcal/mol
Surface area35330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.638, 72.929, 124.189
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein GFP-like fluorescent chromoprotein FP538 / zFP538


Mass: 7403.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U6Y4
#2: Protein GFP-like fluorescent chromoprotein FP538 / zFP538


Mass: 19030.844 Da / Num. of mol.: 2 / Mutation: M129V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zoanthus sp. (invertebrata) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9U6Y4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsOriginally it is a fluorescent protein composed of one polypeptide (Chain C and A, Chain D and B in ...Originally it is a fluorescent protein composed of one polypeptide (Chain C and A, Chain D and B in one chain). Amino acids are broken during chromophore generation.
Has ligand of interestN
Sequence detailsResidue 65 is PHE. It is transformed into NFA during chromophore generation.

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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: 40.99 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / Details: imidazole,PEG 8000, calcium acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13421 / % possible obs: 94 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.272 / Rrim(I) all: 0.13 / Net I/σ(I): 10.43
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 619 / Rpim(I) all: 0.272 / Rrim(I) all: 0.469 / % possible all: 90.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y8Q

5y8q


Resolution: 2.6→26.42 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.873 / SU B: 14.76 / SU ML: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.372
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.215 672 5 %RANDOM
Rwork0.2034 ---
obs0.2061 12678 93.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 76.92 Å2 / Biso mean: 31.635 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å2-0 Å2
2--0.06 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 2.6→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3604 0 0 54 3658
Biso mean---24.24 -
Num. residues----449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133704
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173386
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.674986
X-RAY DIFFRACTIONr_angle_other_deg1.1841.6047902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5235441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38323.488172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.25415643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2441512
X-RAY DIFFRACTIONr_chiral_restr0.0610.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024073
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02781
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 50 -
Rwork0.315 876 -
all-926 -
obs--89.38 %

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