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- PDB-2aha: Crystal structure analysis of a rate-enhanced variant of redox-se... -

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Basic information

Entry
Database: PDB / ID: 2aha
TitleCrystal structure analysis of a rate-enhanced variant of redox-sensitive green fluorescent protein in the reduced form, roGFP1-R8.
ComponentsGreen fluorescent protein
KeywordsLUMINESCENT PROTEIN / beta barrel / chromophore / disulfide
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: 1.98 Å
AuthorsCannon, M.B. / Remington, S.J.
CitationJournal: Protein Sci. / Year: 2006
Title: Re-engineering redox-sensitive green fluorescent protein for improved response rate.
Authors: Cannon, M.B. / Remington, S.J.
History
DepositionJul 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Structure summary
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1896
Polymers53,8052
Non-polymers3844
Water3,441191
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9982
Polymers26,9021
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1904
Polymers26,9021
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.6930, 79.6930, 166.7790
Angle α, β, γ (deg.)90, 90, 120
Int Tables number152
Space group name H-MP3121
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit.

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Components

#1: Protein Green fluorescent protein


Mass: 26902.295 Da / Num. of mol.: 2 / Fragment: GFP / Mutation: Q80R,C48S,S147C,Q204C,K41D,F223R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pRSET-b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium phosphate/citrate, ammonium sulfate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 45664 / Num. obs: 45355 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.141 / Χ2: 8.694
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 99.9 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 50.7 / Num. measured obs: 4462 / Χ2: 3.323 / % possible all: 99.9

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Phasing

Phasing MRRfactor: 0.537 / Cor.coef. Fo:Fc: 0.285
Highest resolutionLowest resolution
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
EPMR2.5phasing
TNTrefinement
PDB_EXTRACT1.601data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EMA

1ema


Resolution: 1.98→50 Å / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4530 -RANDOM
Rwork0.199 ---
all0.204 45664 --
obs0.204 45346 99 %-
Solvent computationBsol: 150 Å2 / ksol: 0.8 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.78 Å22.78 Å20 Å2
2--2.78 Å20 Å2
3----5.57 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 20 191 3667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.6
X-RAY DIFFRACTIONt_bond_d0.013
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs
1.98-2.060.27X-RAY DIFFRACTION4389
2.06-2.150.27X-RAY DIFFRACTION4517
2.15-2.250.26X-RAY DIFFRACTION4459
2.25-2.380.25X-RAY DIFFRACTION4517
2.38-2.540.24X-RAY DIFFRACTION4520
2.54-2.770.23X-RAY DIFFRACTION4531
2.77-3.10.22X-RAY DIFFRACTION4540
3.1-3.670.18X-RAY DIFFRACTION4595
3.67-5.290.15X-RAY DIFFRACTION4600
5.29-500.19X-RAY DIFFRACTION4678

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