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- PDB-1emc: GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT -

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Basic information

Entry
Database: PDB / ID: 1emc
TitleGREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENCE / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPalm, G. / Zdanov, A. / Wlodawer, A.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The structural basis for spectral variations in green fluorescent protein.
Authors: Palm, G.J. / Zdanov, A. / Gaitanaris, G.A. / Stauber, R. / Pavlakis, G.N. / Wlodawer, A.
History
DepositionMar 31, 1997Processing site: BNL
Revision 1.0Aug 20, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 16, 2014Group: Structure summary
Revision 1.4Jan 21, 2015Group: Structure summary
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_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
C: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)107,7654
Polymers107,7654
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.000, 52.000, 103.000
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.135, 0.9908, -0.0056), (0.9905, -0.1348, 0.0252), (0.0242, -0.0089, -0.9997)-17.5576, -31.6102, -7.473
2given(0.9996, 0.011, 0.0246), (-0.0111, 0.9999, 0.0055), (-0.0245, -0.0058, 0.9997)8.8193, 4.4932, -50.5404
3given(0.1316, 0.9913, 0.0013), (0.9913, -0.1316, 0.0048), (0.0049, 0.0007, -1)-11.738, -22.8007, 43.9227

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN / / GFP


Mass: 26941.283 Da / Num. of mol.: 4 / Mutation: INS(A1[B]), F64L, I167T, K238N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Plasmid: PFRED11 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): SG11 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsGYS: [(4Z)-2-[(1R)-1-AMINO-2-HYDROXYETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1- ...GYS: [(4Z)-2-[(1R)-1-AMINO-2-HYDROXYETHYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID. THE CHROMOPHORE IS PART OF THE PEPTIDE CHAIN BETWEEN RESIDUES 64 AND 68.

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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: 2.25 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP METHOD. PROTEIN SOLUTION: 14 MG/ML IN 20 MM KPO4, PH 7.0 WELL SOLUTION: 60% MPD, 50MM TRISCL, PH 8.0 PROTEIN:WELL 1:1, vapor diffusion - hanging drop
PH range: 7.0-8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: protein solution is mixed in a 1:1 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
220 mM1dropKPO4
360 %MPD1reservoir
450 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 12, 1995 / Details: MIRROR
RadiationMonochromator: NI / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 31013 / % possible obs: 78.5 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.078 / Net I/σ(I): 6.5
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 1.9 / Rsym value: 0.253 / % possible all: 56.9
Reflection
*PLUS
Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 56.9 % / Rmerge(I) obs: 0.253

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2.3→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: PARAMETERS FOR THE CHROMOPHORE WERE ESTIMATED ACCORDING TO A MODEL COMPOUND (B.TINANT ET AL., CRYST. STRUCT. COMM., 1980, 9, 671-674). ATOMS CA, CB, OG1, AND CG2 OF THR ? 203 ? WERE REFINED ...Details: PARAMETERS FOR THE CHROMOPHORE WERE ESTIMATED ACCORDING TO A MODEL COMPOUND (B.TINANT ET AL., CRYST. STRUCT. COMM., 1980, 9, 671-674). ATOMS CA, CB, OG1, AND CG2 OF THR ? 203 ? WERE REFINED IN TWO ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.288 2211 7 %RANDOM
Rwork0.205 ---
obs0.205 31013 72.5 %-
Displacement parametersBiso mean: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 0 158 7338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.984
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.53
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.611.5
X-RAY DIFFRACTIONx_mcangle_it2.762
X-RAY DIFFRACTIONx_scbond_it2.612
X-RAY DIFFRACTIONx_scangle_it2.762.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)Weight Biso
11RESTRAINTSX-RAY DIFFRACTION3.570.10692
22X-RAY DIFFRACTION5.310.24724
33X-RAY DIFFRACTION4.560.31186
44X-RAY DIFFRACTION4.530.38996
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.338 167 3.14 %
Rwork0.27 2319 -
obs--46.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR_CSY.PROTOP_CSY.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.53
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.67
LS refinement shell
*PLUS
Rfactor obs: 0.27

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