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- PDB-3kpx: Crystal Structure Analysis of photoprotein clytin -

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Basic information

Entry
Database: PDB / ID: 3kpx
TitleCrystal Structure Analysis of photoprotein clytin
ComponentsApophotoprotein clytin-3
KeywordsFLUORESCENT PROTEIN / HYDROLASE / photoprotein clytin
Function / homology
Function and homology information


Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / bioluminescence / calcium ion binding
Similarity search - Function
EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair ...EF hand / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
C2-HYDROPEROXY-COELENTERAZINE / Apophotoprotein clytin-3
Similarity search - Component
Biological speciesClytia gregaria (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsTitushin, M.S. / Li, Y. / Stepanyuk, G.A. / Wang, B.-C. / Lee, J. / Vysotski, E.S. / Liu, Z.-J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: NMR derived topology of a GFP-photoprotein energy transfer complex
Authors: Titushin, M.S. / Feng, Y. / Stepanyuk, G.A. / Li, Y. / Markova, S.V. / Golz, S. / Wang, B.-C. / Lee, J. / Wang, J. / Vysotski, E.S. / Liu, Z.-J.
History
DepositionNov 17, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Structure summary / Version format compliance
Revision 1.2Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apophotoprotein clytin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9523
Polymers22,4561
Non-polymers4962
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.392, 68.932, 115.348
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

21A-283-

HOH

31A-284-

HOH

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Components

#1: Protein Apophotoprotein clytin-3 / clytin / Apophotoprotein clytin-5 / Apophotoprotein clytin-6


Mass: 22456.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clytia gregaria (invertebrata) / References: UniProt: D7PM14, Renilla-type luciferase
#2: Chemical ChemComp-CZH / C2-HYDROPEROXY-COELENTERAZINE / 8-BENZYL-2-HYDROPEROXY-2-(4-HYDROXY-BENZYL)-6-(4-HYDROXY-PHENYL)-2H-IMIDAZO[1,2-A]PYRAZIN-3-ONE


Mass: 455.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H21N3O5
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.92 Å3/Da / Density % sol: 35.95 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.899→50 Å / Num. all: 14088 / Num. obs: 14018 / % possible obs: 99.5 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F8P

2f8p


Resolution: 1.899→20.306 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.876 / SU ML: 0.26 / σ(F): 1.34 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 696 4.97 %
Rwork0.1707 13294 -
obs0.1731 13990 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.84 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 58.16 Å2 / Biso mean: 19.122 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.651 Å20 Å2-0 Å2
2--0.555 Å2-0 Å2
3----1.206 Å2
Refinement stepCycle: LAST / Resolution: 1.899→20.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 34 128 1678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111592
X-RAY DIFFRACTIONf_angle_d1.1862152
X-RAY DIFFRACTIONf_chiral_restr0.082216
X-RAY DIFFRACTIONf_plane_restr0.011278
X-RAY DIFFRACTIONf_dihedral_angle_d17.516587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8989-2.04540.28051340.22352589X-RAY DIFFRACTION98
2.0454-2.25090.22081470.16362604X-RAY DIFFRACTION100
2.2509-2.57610.2121350.15452654X-RAY DIFFRACTION100
2.5761-3.24350.24431550.16392641X-RAY DIFFRACTION100
3.2435-20.30730.18121250.16342806X-RAY DIFFRACTION100

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