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- PDB-1emb: GREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREA VICTORIA, GLN 80 RE... -

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Basic information

Entry
Database: PDB / ID: 1emb
TitleGREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREA VICTORIA, GLN 80 REPLACED WITH ARG
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / BETA-BARREL
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: 2.13 Å
AuthorsBrejc, K. / Sixma, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structural basis for dual excitation and photoisomerization of the Aequorea victoria green fluorescent protein.
Authors: Brejc, K. / Sixma, T.K. / Kitts, P.A. / Kain, S.R. / Tsien, R.Y. / Ormo, M. / Remington, S.J.
#1: Journal: Science / Year: 1996
Title: Crystal Structure of the Aequorea Victoria Green Fluorescent Protein
Authors: Ormo, M. / Cubitt, A.B. / Kallio, K. / Gross, L.A. / Tsien, R.Y. / Remington, S.J.
History
DepositionJan 8, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9451
Polymers26,9451
Non-polymers00
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.900, 63.200, 68.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / / GFP


Mass: 26945.383 Da / Num. of mol.: 1 / Mutation: Q80R
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE CONTAINING PROTEIN 65 - 67 DENOTED AS CRO
Source: (gene. exp.) Aequorea victoria (jellyfish) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.09 Å3/Da / Density % sol: 41 %
Crystal growpH: 3.8
Details: PROTEIN WAS CRYSTALLIZED FROM 50 MM KH2PO4 AND 20 % (W/V) PEG 8000, PH 3.8.
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlGFP1drop
27 mMTris1drop
30.01 %1dropNaN3
40.01 M1dropKH2PO4
50.03 %(w/v)PEG80001drop
60.05 M1reservoirKH2PO4
720 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.13→20 Å / Num. obs: 13001 / % possible obs: 91.3 % / Observed criterion σ(I): 3 / Redundancy: 4.8 % / Rsym value: 0.061 / Net I/σ(I): 7.1
Reflection shellResolution: 2.13→2.2 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.186 / % possible all: 54.5
Reflection
*PLUS
Num. measured all: 60182 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 54.5 % / Rmerge(I) obs: 0.186

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Processing

Software
NameClassification
TNTrefinement
MOSFLMdata reduction
CCP4data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 2.13→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rfree0.25 607 5 %
Rwork0.196 --
all-12458 -
obs-13001 90 %
Solvent computationBsol: 145.5 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2.13→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 0 74 1907
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01118770.8
X-RAY DIFFRACTIONt_angle_deg1.53425313
X-RAY DIFFRACTIONt_dihedral_angle_d19.50810960
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006562
X-RAY DIFFRACTIONt_gen_planes0.0142656
X-RAY DIFFRACTIONt_it2.32718495
X-RAY DIFFRACTIONt_nbd0.0321110
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.196 / Rfactor Rfree: 0.254
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0062
X-RAY DIFFRACTIONt_plane_restr0.0146

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