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- PDB-1rmo: Probing the Role of Tryptophans in Aequorea Victoria Green Fluore... -

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Basic information

Entry
Database: PDB / ID: 1rmo
TitleProbing the Role of Tryptophans in Aequorea Victoria Green Fluorescent Proteins with an Expanded Genetic Code
Componentswunen-nonfunctional GFP fusion protein
KeywordsLUMINESCENT PROTEIN / Beta-barrel / GFP / Noncanonical amino acid
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: 1.8 Å
AuthorsBudisa, N. / Pal, P.P. / Alefelder, S. / Birle, P. / Krywcun, T. / Rubini, M. / Wenger, W. / Bae, J.H. / Steiner, T.
CitationJournal: Biol.Chem. / Year: 2004
Title: Probing the role of tryptophans in Aequorea victoria green fluorescent proteins with an expanded genetic code
Authors: Budisa, N. / Pal, P.P. / Alefelder, S. / Birle, P. / Krywcun, T. / Rubini, M. / Wenger, W. / Bae, J.H. / Steiner, T.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_ref_seq_dif.details
Revision 1.4Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: wunen-nonfunctional GFP fusion protein


Theoretical massNumber of molelcules
Total (without water)26,8311
Polymers26,8311
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.793, 62.773, 70.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein wunen-nonfunctional GFP fusion protein / Cyan Fluorescent Protein


Mass: 26831.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: [3,2]Tpa-containing / Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid details: plasmid bought from BD Clontech / Plasmid: pECFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 14% PEG 1000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 2001
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→17.69 Å / Num. all: 21939 / Num. obs: 20540 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 14.7 Å2
Reflection shellResolution: 1.8→1.89 Å / % possible all: 92.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMG

1emg


Resolution: 1.8→17.69 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1616341.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2046 10 %RANDOM
Rwork0.185 ---
all0.222 20540 --
obs0.1851 18494 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.8698 Å2 / ksol: 0.348582 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2---0.9 Å20 Å2
3---0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.8→17.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 0 64 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006525
X-RAY DIFFRACTIONc_angle_deg1.43545
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d1.38
X-RAY DIFFRACTIONc_mcbond_it4.871.5
X-RAY DIFFRACTIONc_mcangle_it6.092
X-RAY DIFFRACTIONc_scbond_it12.592
X-RAY DIFFRACTIONc_scangle_it16.392.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 343 10.8 %
Rwork0.227 2836 -
obs--88.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION2PRO_CRO_SULPRO_CRO_SUL
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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