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- PDB-2gw4: Crystal structure of stony coral fluorescent protein Kaede, red form -

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Basic information

Entry
Database: PDB / ID: 2gw4
TitleCrystal structure of stony coral fluorescent protein Kaede, red form
Components(Kaede) x 2
KeywordsLUMINESCENT PROTEIN / BETA BARREL
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
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, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich ...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, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / : / Kaede
Similarity search - Component
Biological speciesTrachyphyllia geoffroyi (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 Å
AuthorsHayashi, I. / Mizuno, H. / Miyawako, A. / Ikura, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystallographic evidence for water-assisted photo-induced peptide cleavage in the stony coral fluorescent protein Kaede.
Authors: Hayashi, I. / Mizuno, H. / Tong, K.I. / Furuta, T. / Tanaka, F. / Yoshimura, M. / Miyawaki, A. / Ikura, M.
History
DepositionMay 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: 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 / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_poly / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_torsion / struct_conn / struct_conn_type / 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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The residues His 62, Tyr 63 and Gly 64 constitute the chromophore CR8

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kaede
B: Kaede
C: Kaede
D: Kaede
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9508
Polymers51,7154
Non-polymers2354
Water7,873437
1
A: Kaede
B: Kaede
C: Kaede
D: Kaede
hetero molecules

A: Kaede
B: Kaede
C: Kaede
D: Kaede
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,90016
Polymers103,4318
Non-polymers4708
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area28350 Å2
ΔGint-180 kcal/mol
Surface area32550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.197, 81.169, 53.512
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein Kaede


Mass: 6894.060 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trachyphyllia geoffroyi (invertebrata) / Plasmid: pRSETb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 23503508, UniProt: Q8I6J8*PLUS
#2: Protein Kaede


Mass: 18963.568 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trachyphyllia geoffroyi (invertebrata) / Plasmid: pRSETb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 23503508, UniProt: Q8I6J8*PLUS
#3: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2M Li2SO4, 2mM NiCl2, 0.1M Tris, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU
DetectorDetector: IMAGE PLATE / Date: Oct 20, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 68143

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Processing

Software
NameClassification
MOSFLMdata reduction
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 1.6→25 Å / σ(F): 0 /
RfactorNum. reflection
Rfree0.213 -
Rwork0.198 -
obs-67774
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3552 0 4 437 3993
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_kr.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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