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- PDB-2zo7: Crystal Structure of a Kusabira-Cyan Mutant (KCY-R1), a Cyan/Gree... -

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Basic information

Entry
Database: PDB / ID: 2zo7
TitleCrystal Structure of a Kusabira-Cyan Mutant (KCY-R1), a Cyan/Green-Emitting GFP-Like Protein
ComponentsCYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)
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: 1.58 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: 2EJI
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 / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)


Theoretical massNumber of molelcules
Total (without water)24,8821
Polymers24,8821
Non-polymers00
Water5,747319
1
A: CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)

A: CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)


Theoretical massNumber of molelcules
Total (without water)49,7642
Polymers49,7642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2510 Å2
ΔGint-11 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.689, 45.016, 51.158
Angle α, β, γ (deg.)90.00, 94.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

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Components

#1: Protein CYAN/GREEN-EMITTING GFP-LIKE PROTEIN, KUSABIRA-CYAN MUTANT (KCY-R1)


Mass: 24882.207 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-220
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.: 319 / 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 -2- ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. RESIDUES -2-0 AND 221 ARE EXPRESSION TAGS. THE DIFFERENCE BETWEEN THE SEQUENCE DATABASE THAT WILL BE DEPOSITED AT A LATER TIME AND THE COORDINATES IS THAT GYS 64 REPRESENTS THE CHROMOPHORE (SER-TYR-GLY). RESIDUES SER 63, TYR 64 AND GLY 65 ARE LABELLED AS RESIDUE 64 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 35-40% PEG 8000, 0.2M (NH4)2SO4, 0.1M SODIUM CACODYLATE, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Jun 15, 2005
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 29798 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.58→1.64 Å / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5 / % possible all: 91.7

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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 2ZO6

2zo6


Resolution: 1.58→18.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1077645.55 / 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
Rfree0.207 1410 4.7 %RANDOM
Rwork0.178 ---
obs0.178 29784 98.4 %-
all-29798 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.5 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.68 Å20 Å24.31 Å2
2--4.89 Å20 Å2
3---2.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.58→18.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1734 0 0 319 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 1.58→1.68 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.224 182 3.7 %
Rwork0.227 4721 -
obs--97.9 %
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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