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- PDB-1hcj: Photoproduct of the wild-type Aequorea victoria Green Fluorescent... -

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Basic information

Entry
Database: PDB / ID: 1hcj
TitlePhotoproduct of the wild-type Aequorea victoria Green Fluorescent Protein
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / FLUORESCENT PROTEIN / BETA-BARREL / BIOLUMINESCENCE / LUMINESCENCE
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: 1.8 Å
AuthorsVan Thor, J.J. / Gensch, T. / Hellingwerf, K.J. / Johnson, L.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Phototransformation of Green Fluorescent Protein with Uv and Visible Light Leads to Decarboxylation of Glutamate 222
Authors: Van Thor, J.J. / Gensch, T. / Hellingwerf, K.J. / Johnson, L.
History
DepositionMay 4, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2001Provider: 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 / pdbx_validate_torsion / 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 SHEET PRESENTED FOR EACH CHAIN ON SHEET RECORDS BELOW IS ... SHEET DETERMINATION METHOD: DSSP THE SHEET PRESENTED FOR EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THAT 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

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
Water11,403633
1
A: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN

A: GREEN FLUORESCENT PROTEIN
D: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)107,5494
Polymers107,5494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area6150 Å2
ΔGint-44.8 kcal/mol
Surface area44060 Å2
MethodPQS
2
B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN

B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)107,5494
Polymers107,5494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Buried area6230 Å2
ΔGint-15.6 kcal/mol
Surface area43750 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.770, 65.670, 110.500
Angle α, β, γ (deg.)90.00, 103.88, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
GREEN FLUORESCENT PROTEIN / / GFP


Mass: 26887.346 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Gene: GFP / Organ: PHOTOGENIC ORGAN / Cellular location (production host): CYTOPLASM / Gene (production host): GFP / Production host: ESCHERICHIA COLI M15 (bacteria) / References: UniProt: P42212
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMUTATION GLN80ARG OTHER_DETAILS: THE CHROMOPHORE, P-HYDROXYBENZYLIDENE-IMIDAZOLIDINONE (GYS), IS ...MUTATION GLN80ARG OTHER_DETAILS: THE CHROMOPHORE, P-HYDROXYBENZYLIDENE-IMIDAZOLIDINONE (GYS), IS AUTO-CATALYTICALLY FORMED VIA CYCLISATION IN THE TRIPEPTIDE SER65-TYR66-GLY67
Sequence detailsMODRES: 1HCJ GYS A 66() GLU 222 SIDECHAIN IS SPECIFICALLY DECARBOXYLATED AS A RESULT OF ...MODRES: 1HCJ GYS A 66() 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: 2.34 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.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
220 mMTris-Cl1droppH7.8
30.01 %(w/v)1dropNaN3
450 mM1reservoirMgCl2
514-17 %(w/v)PEG33501reservoir
650-100 mMTris-Cl1reservoirpH7.8-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: SAGITALLY FOCUSING GE(220
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.8→33.15 Å / Num. obs: 92677 / % possible obs: 97.6 % / Observed criterion σ(I): 1.5 / Redundancy: 1.9 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.251 / Mean I/σ(I) obs: 2.7 / % possible all: 96.8
Reflection
*PLUS
Num. measured all: 519063
Reflection shell
*PLUS
% possible obs: 96.8 %

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GFL

1gfl


Resolution: 1.8→33.15 Å / SU B: 3.82 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.151
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4504 5 %RANDOM
Rwork0.209 ---
obs-92677 97.6 %-
Displacement parametersBiso mean: 32.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7246 0 0 633 7879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0770.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.882
X-RAY DIFFRACTIONp_mcangle_it2.543
X-RAY DIFFRACTIONp_scbond_it2.512
X-RAY DIFFRACTIONp_scangle_it3.73
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0290.0137
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1650.3
X-RAY DIFFRACTIONp_planar_tor9.97
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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