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- PDB-1cv7: Crystal structure of enhanced cyan-emission variant of GFP -

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Basic information

Entry
Database: PDB / ID: 1cv7
TitleCrystal structure of enhanced cyan-emission variant of GFP
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / GREEN FLUORESCENT PROTEIN / BIOLUMINESCENCE / PHOTOACTIVE PROTEIN / FLUORESCENT TAG
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 / Resolution: 2.5 Å
AuthorsO'Brien, P. / Elsliger, M.A. / Kallio, K. / Remington, S.J.
CitationJournal: To be Published / Year: 1999
Title: Crystal Structure of Enhanced Cyan-Emission Variant od GFP
Authors: O'Brien, P. / Elsliger, M.A. / Kallio, K. / Remington, S.J.
History
DepositionAug 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 3, 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

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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)25,7081
Polymers25,7081
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.052, 62.781, 66.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein GREEN FLUORESCENT PROTEIN / / CYAN-EMISSION VARIANT OF GFP


Mass: 25707.936 Da / Num. of mol.: 1 / Mutation: K26R,F64L,S65T,Y66W,N146I,M153T,V163A,N164H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Description: THE N-TERMINAL HIS-TAG HAS BEEN REMOVED / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 (DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.21 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12% PEG-1550, 50mM calcium acetate and 100 mM acetaete buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→19.5 Å / Num. all: 8068 / Num. obs: 7829 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 2.93
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.611 / Num. unique all: 511 / % possible all: 95.5

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Processing

Software
NameClassification
SCALEPACKdata scaling
TNTrefinement
TNTphasing
RefinementResolution: 2.5→19.5 Å / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.186 --
obs0.1861 7829 97.4 %
all-8068 -
Refinement stepCycle: LAST / Resolution: 2.5→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 30 1768
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_bond_d0.013

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