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- PDB-1w7u: Photoproduct of the Wild-Type Aequorea victoria Green Fluorescent... -

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Basic information

Entry
Database: PDB / ID: 1w7u
TitlePhotoproduct of the Wild-Type Aequorea victoria Green Fluorescent Protein after structural annealing at 170K
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / PHOTOPRODUCT
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVan Thor, J.J. / Georgiev, G.Y. / Towrie, M. / Sage, J.T.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Ultrafast and Low Barrier Motions in the Photoreactions of the Green Fluorescent Protein
Authors: Van Thor, J.J. / Georgiev, G.Y. / Towrie, M. / Sage, J.T.
History
DepositionSep 9, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2014Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 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 / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.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
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 12-STRANDED BARRELS REPRESENTED BY A 13-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" AND "DA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 10-STRANDED BARRELS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)107,5494
Polymers107,5494
Non-polymers00
Water16,520917
1
A: GREEN FLUORESCENT PROTEIN
B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN

A: GREEN FLUORESCENT PROTEIN
B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)215,0998
Polymers215,0998
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area14910 Å2
ΔGint-75.4 kcal/mol
Surface area88870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)155.273, 52.705, 141.746
Angle α, β, γ (deg.)90.00, 119.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN


Mass: 26887.346 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE CHROMOPHORE (GYS, 5-(1-AMINO-2-HYDROXYETHYL)-1-CARBOXYMETHYL-3-((P-HYDROXYPHENYL)-METHYLENE)-IMIDAZOL-2-ONE)IS PART OF THE PEPTIDE CHAIN BETWEEN RESIDUES 64 AND 68.
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Organ: PHOTOGENIC ORGAN / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 917 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A, B, C, D, GLN 80 ARG
Sequence detailsMODRES: GLU 222 SIDECHAIN IS SPECIFICALLY DECARBOXYLATED AS A RESULT OF PHOTOTRANSFORMATION. OE1, ...MODRES: GLU 222 SIDECHAIN IS SPECIFICALLY DECARBOXYLATED AS A RESULT OF PHOTOTRANSFORMATION. OE1, OE2, CD ATOMS ARE NOT PRESENT FOR THIS RESIDUE IN ALL CHAINS

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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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / pH: 7.8
Details: CRYSTALS WERE GROWN AT 4C FROM 50 MM MGCL2, 14-17 % PEG3350 AND 50-100 MM TRIS/CL PH 7.8 - 8.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97809
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2003 / Details: RH COATED SILICON MIRROR
RadiationMonochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97809 Å / Relative weight: 1
ReflectionResolution: 1.85→33.15 Å / Num. obs: 85637 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.8 / % possible all: 84

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HCJ

1hcj


Resolution: 1.85→119.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.84 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4166 5 %RANDOM
Rwork0.179 ---
obs0.182 79055 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.04 Å2
2--0.56 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7302 0 0 917 8219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217476
X-RAY DIFFRACTIONr_bond_other_d0.0020.026562
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.95610099
X-RAY DIFFRACTIONr_angle_other_deg1.231315416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4725899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1320.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028277
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021475
X-RAY DIFFRACTIONr_nbd_refined0.250.21234
X-RAY DIFFRACTIONr_nbd_other0.2630.27811
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.24422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2668
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1440.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3750.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8181.54488
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.62627258
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.66432988
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4374.52840
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 242
Rwork0.198 4554

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