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- PDB-2wur: Atomic resolution structure of GFP measured on a rotating anode -

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Basic information

Entry
Database: PDB / ID: 2wur
TitleAtomic resolution structure of GFP measured on a rotating anode
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE / BETA-BARREL / LUMINESCENCE / PHOTOPROTEIN / 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
ETHANOL / ISOPROPYL ALCOHOL / Green fluorescent protein
Similarity search - Component
Biological speciesAEQUOREA VICTORIA (jellyfish)
MethodX-RAY DIFFRACTION / SAD / Resolution: 0.9 Å
AuthorsPalm, G.J. / Schierbeek, A.J. / Kloos, M.
Citation
Journal: J.Am.Chem.Soc. / Year: 2010
Title: Visualizing Proton Antenna in a High-Resolution Green Fluorescent Protein Structure.
Authors: Shinobu, A. / Palm, G.J. / Schierbeek, A.J. / Agmon, N.
#1: Journal: 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
DepositionOct 7, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GREEN FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2539
Polymers26,8701
Non-polymers3838
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.987, 59.050, 67.700
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 /


Mass: 26870.207 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CHROMOPHORE FORMED BY RESIDUES 65-67 / Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P42212
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLN 80 TO ARG ...ENGINEERED RESIDUE IN CHAIN A, PHE 64 TO LEU ENGINEERED RESIDUE IN CHAIN A, GLN 80 TO ARG ENGINEERED RESIDUE IN CHAIN A, ILE 167 TO THR ENGINEERED RESIDUE IN CHAIN A, LYS 238 TO ASN
Nonpolymer detailsGYS: THE CHROMOPHORE (GYS) IS FORMED FROM SER 65 - TYR 66 - GLY 67 BY CYCLIZATION OF THE ...GYS: THE CHROMOPHORE (GYS) IS FORMED FROM SER 65 - TYR 66 - GLY 67 BY CYCLIZATION OF THE POLYPEPTIDE BACKBONE BETWEEN NITROGEN OF GLY 67 AND CARBONYL CARBON OF SER 65. SUBSEQUENTLY THE CARBONYL OXYGEN IS ELIMINATED AS WATER AND TYR 66 IS OXIDIZED TO DEHYDROTYROSINE.

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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 Å3/Da / Density % sol: 39 % / Description: SAD WAS BASED ON THE SULFUR SIGNAL UP TO 1.5 A
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOR DIFFUSION: 2 UL PROTEIN (10 MG/ML IN 20 MM TRIS, PH 8.0) PLUS 2 UL RESERVOIR (40% ETHANOL, 10 % DIOXANE)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 20, 2004 / Details: MONTEL MULTILAYER OPTIC
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 0.9→68 Å / Num. obs: 155426 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 19.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.35
Reflection shellResolution: 0.9→1 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 90.3

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Processing

Software
NameVersionClassification
SHELXL-97refinement
SAINTdata reduction
SADABSdata scaling
SHELXDSHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 0.9→6 Å / Num. parameters: 20655 / Num. restraintsaints: 26011 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03.THERE ARE MANY WEAK REFLECTIONS WHICH ARE REMOVED IN THE CALCULATION OF REFLECTIONS WITH F>4SIG(F). THERE ARE MORE REFLECTIONS WITH ...Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.03.THERE ARE MANY WEAK REFLECTIONS WHICH ARE REMOVED IN THE CALCULATION OF REFLECTIONS WITH F>4SIG(F). THERE ARE MORE REFLECTIONS WITH F>0SIG(F) NUMBERING OF THE WATER MOLECULES IS SHIFTED BY 2000 COMPARED TO THE NUMBERS USED IN THE REFERENCE LISTED IN JRNL.
RfactorNum. reflection% reflectionSelection details
Rfree0.174 4231 3 %RANDOM
all0.1456 133320 --
obs--90.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 29 / Occupancy sum hydrogen: 1814.6 / Occupancy sum non hydrogen: 2160.4
Refinement stepCycle: LAST / Resolution: 0.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 25 318 2164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.034
X-RAY DIFFRACTIONs_angle_d0.052
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0329
X-RAY DIFFRACTIONs_zero_chiral_vol0.145
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.148
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.015
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.042
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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