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- PDB-2g6y: Crystal structure of the novel green fluorescent protein from mar... -

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Basic information

Entry
Database: PDB / ID: 2g6y
TitleCrystal structure of the novel green fluorescent protein from marine copepod Pontellina plumata
Componentsgreen fluorescent protein 2
KeywordsLUMINESCENT PROTEIN / green fluorescent protein / natural chromophore / rapid maturation / beta-can
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
: / Green fluorescent protein 2
Similarity search - Component
Biological speciesPontellina plumata (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsEvdokimov, A.G. / Pokross, M.E. / Chudakov, D.M.
CitationJournal: Embo Rep. / Year: 2006
Title: Structural basis for the fast maturation of Arthropoda green fluorescent protein.
Authors: Evdokimov, A.G. / Pokross, M.E. / Egorov, N.S. / Zaraisky, A.G. / Yampolsky, I.V. / Merzlyak, E.M. / Shkoporov, A.N. / Sander, I. / Lukyanov, K.A. / Chudakov, D.M.
History
DepositionFeb 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 999;SEQUENCE Residues GLY 57, TYR 58 and GLY 59 constitute the chromophore CR2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: green fluorescent protein 2
B: green fluorescent protein 2
C: green fluorescent protein 2
D: green fluorescent protein 2


Theoretical massNumber of molelcules
Total (without water)97,5774
Polymers97,5774
Non-polymers00
Water15,961886
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6640 Å2
ΔGint-54 kcal/mol
Surface area32570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.007, 97.160, 75.153
Angle α, β, γ (deg.)90.00, 96.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
green fluorescent protein 2


Mass: 24394.172 Da / Num. of mol.: 4
Mutation: K5E, V117M, V149D, V151D, A155T, F168S, L200D, I219D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pontellina plumata (crustacean) / Gene: ppluGFP2 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: GenBank: 33243028, UniProt: Q6WV12*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 886 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.25 M sodium malonate, 100 mM sodium acetate, 2.2 M ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 2005 / Details: silicon
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→29.74 Å / Num. all: 122154 / Num. obs: 122154 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 16.77
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.47 / Num. unique all: 19165 / % possible all: 90.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.556 / SU ML: 0.057 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 6137 5 %RANDOM
Rwork0.162 ---
all0.165 122154 --
obs0.162 122152 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20.41 Å2
2--0.76 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 0 886 7704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0217284
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9499899
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6725942
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18723.528360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.616151187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3831542
X-RAY DIFFRACTIONr_chiral_restr0.1240.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025752
X-RAY DIFFRACTIONr_nbd_refined0.2160.23291
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2677
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.229
X-RAY DIFFRACTIONr_mcbond_it2.4191.54477
X-RAY DIFFRACTIONr_mcangle_it3.42427097
X-RAY DIFFRACTIONr_scbond_it4.97533326
X-RAY DIFFRACTIONr_scangle_it6.8224.52754
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 423 -
Rwork0.191 7655 -
obs-8078 85.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29470.0894-0.0660.1524-0.02370.3053-0.0097-0.01980.0213-0.0093-0.01590.02990.0010.01060.0255-0.02580.00030.0027-0.01970.00810.0182-11.874314.632921.0373
20.2232-0.0509-0.30430.17360.01270.67420.0084-0.0410.0562-0.0120.0487-0.05820.01740.0832-0.0571-0.02830.00170.0018-0.0061-0.02270.024617.900714.294323.3652
30.3416-0.1555-0.07020.51280.34340.6874-0.0361-0.0683-0.00450.00570.0989-0.07540.04150.0598-0.0627-0.03190.0131-0.0063-0.0137-0.0090.003116.4788-16.376523.2567
40.1688-0.1197-0.15470.42560.11570.3150.01870.0176-0.0391-0.0241-0.05280.0529-0.0323-0.03660.0341-0.02110.00950.0017-0.0248-0.00470.0122-10.2023-13.62389.4415
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA3 - 2183 - 216
22BB1 - 2181 - 216
33CC2 - 2192 - 217
44DD3 - 2193 - 217

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