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- PDB-2dd7: A GFP-like protein from marine copepod, Chiridius poppei -

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Basic information

Entry
Database: PDB / ID: 2dd7
TitleA GFP-like protein from marine copepod, Chiridius poppei
Componentsgreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / Beta Barrel / Mainly Beta / Green fluorescent protein
Function and homology information
Biological speciesChiridius poppei (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSuto, K. / Masuda, H. / Takenaka, Y. / Mizuno, H.
CitationJournal: Genes Cells / Year: 2009
Title: Structural basis for red-shifted emission of a GFP-like protein from the marine copepod Chiridius poppei
Authors: Suto, K. / Masuda, H. / Takenaka, Y. / Tsuji, F.I. / Mizuno, H.
History
DepositionJan 23, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: green fluorescent protein
B: green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4984
Polymers49,2422
Non-polymers2572
Water7,855436
1
A: green fluorescent protein
hetero molecules

A: green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3134
Polymers49,2422
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area17840 Å2
MethodPISA
2
B: green fluorescent protein
hetero molecules

B: green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6844
Polymers49,2422
Non-polymers4432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area2690 Å2
ΔGint-15 kcal/mol
Surface area17500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.478, 133.494, 108.733
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-502-

CL

21A-1401-

HOH

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Components

#1: Protein green fluorescent protein / Yellowish-green fluorescent protein


Mass: 24620.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chiridius poppei (crustacean) / Plasmid: pET-101 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MHN7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsGLY 55, TYR 56 AND GLY 57 ARE MODIFIED TO MAKE CHROMOPHORE (CR2 56).

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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: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.1M CAPS (pH 10.5), 2.2M Ammonium Sulfate, 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97986 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2004
RadiationMonochromator: SILICON (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97986 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 65109 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 9.9 Å2
Reflection shellResolution: 1.9→2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3445681.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3281 5 %RANDOM
Rwork0.204 ---
all-65173 --
obs-65081 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.9488 Å2 / ksol: 0.393849 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.25 Å20 Å2
3----2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 15 436 3891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 569 5.3 %
Rwork0.24 10180 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GYG.paramGYG.top

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