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- PDB-2zo6: Crystal Structure of Kusabira-Cyan (KCY), a Cyan-Emitting GFP-Lik... -

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Basic information

Entry
Database: PDB / ID: 2zo6
TitleCrystal Structure of Kusabira-Cyan (KCY), a Cyan-Emitting GFP-Like Protein
ComponentsCYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY)
KeywordsLUMINESCENT PROTEIN / GFP-LIKE PROTEIN / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesFungia concinna (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsKikuchi, A. / Fukumura, E. / Karasawa, S. / Miyawaki, A. / Shiro, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of a new cyan fluorescent protein and its hue-shifted variants
Authors: Kikuchi, A. / Fukumura, E. / Karasawa, S. / Shiro, Y. / Miyawaki, A.
History
DepositionMay 6, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
SupersessionMay 2, 2012ID: 2EJH
Revision 1.2May 2, 2012Group: Other
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: CYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY)


Theoretical massNumber of molelcules
Total (without water)28,2251
Polymers28,2251
Non-polymers00
Water5,657314
1
A: CYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY)

A: CYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY)


Theoretical massNumber of molelcules
Total (without water)56,4502
Polymers56,4502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.754, 42.804, 50.699
Angle α, β, γ (deg.)90.00, 96.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-378-

HOH

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Components

#1: Protein CYAN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN (KCY)


Mass: 28224.953 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fungia concinna (invertebrata) / Plasmid: PRSET-B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. RESIDUES - ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. RESIDUES -30-0 AND 219-223 ARE EXPRESSION TAGS. THE DIFFERENCE BETWEEN THE SEQUENCE DATABASE THAT WILL BE DEPOSITED AT A LATER TIME AND THE COORDINATES IS THAT GYS 63 REPRESENTS A CHROMOPHORE (SER-TYR-GLY). RESIDUES SER 62, TYR 63 AND GLY 64 ARE LABELLED AS RESIDUE 63 IN THE COORDINATES.

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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: 1.81 Å3/Da / Density % sol: 32.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 3350, 0.2M LICL, 20MM TRIS/HCL, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 23, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 36604 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.042
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3 / % possible all: 62.5

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MOU

1mou


Resolution: 1.4→19.49 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1257321.54 / Data cutoff low absF: 0 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 1823 5 %RANDOM
Rwork0.164 ---
obs0.164 36588 91.4 %-
all-36604 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.58 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.7 Å20 Å2-0.64 Å2
2--10.52 Å20 Å2
3----6.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 314 2015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.051.5
X-RAY DIFFRACTIONc_mcangle_it1.472
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 1.4→1.49 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 211 4.8 %
Rwork0.245 4192 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CRO.PARAMCRO.TOP

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