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- PDB-2ib5: Structural characterization of a blue chromoprotein and its yello... -

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Basic information

Entry
Database: PDB / ID: 2ib5
TitleStructural characterization of a blue chromoprotein and its yellow mutant from the sea anemone cnidopus japonicus
ComponentsChromo protein
KeywordsLUMINESCENT PROTEIN / beta barrel / alpha helix / chromoprotein / chromophore / blue / GFP-like protein
Function / homology
Function and homology information


Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chromo protein
Similarity search - Component
Biological speciesCnidopus japonicus (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsChan, M.C.Y. / Bosanac, I. / Ikura, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Characterization of a Blue Chromoprotein and Its Yellow Mutant from the Sea Anemone Cnidopus Japonicus
Authors: Chan, M.C.Y. / Karasawa, S. / Mizuno, H. / Bosanac, I. / Ho, D. / Prive, G.G. / Miyawaki, A. / Ikura, M.
History
DepositionSep 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromo protein
B: Chromo protein
C: Chromo protein
D: Chromo protein
E: Chromo protein
F: Chromo protein
G: Chromo protein
H: Chromo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,25724
Polymers214,7388
Non-polymers1,52016
Water23,9241328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Chromo protein
B: Chromo protein
C: Chromo protein
D: Chromo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12912
Polymers107,3694
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-118 kcal/mol
Surface area30550 Å2
MethodPISA
3
E: Chromo protein
F: Chromo protein
G: Chromo protein
H: Chromo protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12912
Polymers107,3694
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13510 Å2
ΔGint-119 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.860, 126.850, 100.510
Angle α, β, γ (deg.)90.00, 102.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a octomer generated from the tetramer in the asymmetric unit.

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Components

#1: Protein
Chromo protein / cjBlue


Mass: 26842.227 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cnidopus japonicus (sea anemone) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0AQQ7
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1328 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUES GLN 63, TYR 64 AND GLY 65 ARE MODIFIED TO FORM A CHROMOPHORE (CRQ 65) IN ALL CHAINS. ...RESIDUES GLN 63, TYR 64 AND GLY 65 ARE MODIFIED TO FORM A CHROMOPHORE (CRQ 65) IN ALL CHAINS. RESIDUE LEU 64 WAS ENGINEERED FROM TYR OCCURS NATURALLY.

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaH2PO4, 20mM Tris-HCl, 150mM NaCl, 20% PEG3350, 20% glycerol, 2mM TCEP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: SBC-2 / Detector: CCD / Date: Dec 9, 2004
Details: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 335346 / Num. obs: 335346 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 52.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.1 / Num. unique all: 16336 / % possible all: 92

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.225 8101 -random
Rwork0.195 ---
obs0.195 332364 100 %-
all-332364 --
Displacement parametersBiso mean: 19.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14384 0 80 1328 15792
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_angle_deg1.673
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_mcbond_it1.52
X-RAY DIFFRACTIONc_mcangle_it2.06
X-RAY DIFFRACTIONc_scbond_it3.2
X-RAY DIFFRACTIONc_scangle_it4.36
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.05
RfactorNum. reflection% reflection
Rfree0.26 847 -
Rwork0.22 --
obs--93.3 %

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