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- PDB-1h6r: The oxidized state of a redox sensitive variant of green fluoresc... -

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Basic information

Entry
Database: PDB / ID: 1h6r
TitleThe oxidized state of a redox sensitive variant of green fluorescent protein
ComponentsGREEN FLUORESCENT PROTEIN
KeywordsLUMINESCENT PROTEIN / LUMINESCENCE / GREEN FLUORESCENT PROTEIN / YELLOW-EMISSION
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: 1.5 Å
AuthorsOstergaard, H. / Henriksen, A. / Hansen, F.G. / Winther, J.R.
CitationJournal: Embo J. / Year: 2001
Title: Shedding Light on Disulfide Bond Formation: Engineering a Redox Switch in Green Fluorescent Protein
Authors: Ostergaard, H. / Henriksen, A. / Hansen, F.G. / Winther, J.R.
History
DepositionJun 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Dec 13, 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_site
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_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", "BA", "CA" IN CHAIN A, B, C ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "BA", "CA" IN CHAIN A, B, C RESPECTIVELY ON SHEET RECORDS BELOW ARE 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
B: GREEN FLUORESCENT PROTEIN
C: GREEN FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9045
Polymers80,8333
Non-polymers712
Water15,133840
1
A: GREEN FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9802
Polymers26,9441
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: GREEN FLUORESCENT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9802
Polymers26,9441
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: GREEN FLUORESCENT PROTEIN


Theoretical massNumber of molelcules
Total (without water)26,9441
Polymers26,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.864, 93.915, 140.551
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 / / GFP


Mass: 26944.482 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AEQUOREA VICTORIA (jellyfish) / Tissue: CIRCUMORAL RING CANAL / Description: SYNTHETIC GENE / Organ: PHOTOGENIC ORGAN / Plasmid: PET24 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C ENGINEERED MUTATION SER65ALA,CYS48VAL,VAL68LEU, ...CHAIN A, B, C ENGINEERED MUTATION SER65ALA,CYS48VAL,VAL68LEU, SER72ALA,GLN80ARG,ASN149CYS,MET153VAL,SER202CYS,THR203TYR, ASP234HIS
Sequence detailsMODRES: 1H6R CRO() 66() THE FLUOROPHORE IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE ...MODRES: 1H6R CRO() 66() THE FLUOROPHORE IS GENERATED BY AN AUTOCATALYTIC CYCLIZATION OF THE POLYPEPTIDE BACKBONE OF ALA 65, TYR 66, GLY 67. RESIDUES 65, 66, 67 ARE NOT PRESENT IN THE ENTRY, ARE INSTEAD REPLACED WITH PIA 66.

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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: 2.5 Å3/Da / Density % sol: 49 %
Crystal growpH: 8
Details: 100 MM HEPES, PH 8.0, 100 MM MGCL2, AND 14% PEG4000
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
210 mMHEPES1droppH8.0
3100 mMHEPES1reservoirpH8.0
4100 mM1reservoirMgCl2
514 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0362
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0362 Å / Relative weight: 1
ReflectionResolution: 1.5→78.09 Å / Num. obs: 116321 / % possible obs: 89.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 18.3
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2 / % possible all: 72.9
Reflection
*PLUS
Num. measured all: 750960
Reflection shell
*PLUS
% possible obs: 72.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFP

1yfp


Resolution: 1.5→78.09 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 689676.36 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: A SIGNIFICANT 2FO-FC AND FO-FC DENSITY WAS OBSERVED WITH A CENTER 1.5 ANGSTROM FROM CYS 70 SG AND IT IS POSSIBLE THAT CYS 70 IS IN AN OXIDIZED STATE.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 5546 5 %RANDOM
Rwork0.183 ---
obs0.183 109885 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.493 Å2 / ksol: 0.366229 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å20 Å20 Å2
2--2.38 Å20 Å2
3----1.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→78.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5499 0 2 840 6341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.532.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 778 5.3 %
Rwork0.261 14022 -
obs--72.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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