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- PDB-5wwk: Highly stable green fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 5wwk
TitleHighly stable green fluorescent protein
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / CHROMOPHORE MODIFICATION / THERMAL STABILITY FLUORESCENCE PROTEIN SENSOR
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 / molecular replacement / Resolution: 3.199 Å
AuthorsSriram, R. / George, A. / Kesavan, M. / Jaimohan, S.M. / Kamini, N.R. / Easwaramoorthi, S. / Ganesh, S. / Gunasekaran, K. / Ayyadurai, N.
CitationJournal: J.Phys.Chem.B / Year: 2019
Title: Excited State Electronic Interconversion and Structural Transformation of Engineered Red-Emitting Green Fluorescent Protein Mutant.
Authors: Augustine, G. / Raghavan, S. / NumbiRamudu, K. / Easwaramoorthi, S. / Shanmugam, G. / Seetharani Murugaiyan, J. / Gunasekaran, K. / Govind, C. / Karunakaran, V. / Ayyadurai, N.
History
DepositionJan 2, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
E: Green fluorescent protein
F: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)155,2636
Polymers155,2636
Non-polymers00
Water362
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)25,8771
Polymers25,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.100, 95.976, 269.622
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 2 - 232 / Label seq-ID: 1 - 229

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD
5chain EEE
6chain FFF

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Components

#1: Protein
Green fluorescent protein /


Mass: 25877.188 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Plasmid: pQE80L / Details (production host): Amp resistant / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.38 Å3/Da / Density % sol: 48.3 % / Description: Rod like crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 8000, HEPES pH 8.0, 100 mM Mgcl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2016
RadiationMonochromator: Double Crystal or white beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→29.02 Å / Num. obs: 25406 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.983 / Rmerge(I) obs: 0.361 / Rpim(I) all: 0.101 / Rrim(I) all: 0.375 / Net I/σ(I): 8.9 / Num. measured all: 339416 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.2-3.4213.90.9596230344800.8440.2650.9963.499.7
9.05-29.0212.80.0721580812380.9980.0210.07525.597.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.12 Å29.02 Å
Translation6.12 Å29.02 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.23data scaling
PHASER2.7.16phasing
PDB_EXTRACT3.22data extraction
XDSGPLvdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3D

3v3d


Resolution: 3.199→29.024 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 2547 10.05 %
Rwork0.2207 22795 -
obs0.2261 25342 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.26 Å2 / Biso mean: 37.9127 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 3.199→29.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10932 0 0 2 10934
Biso mean---35.04 -
Num. residues----1374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00811184
X-RAY DIFFRACTIONf_angle_d0.96315095
X-RAY DIFFRACTIONf_chiral_restr0.0581626
X-RAY DIFFRACTIONf_plane_restr0.0061968
X-RAY DIFFRACTIONf_dihedral_angle_d3.7626618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6539X-RAY DIFFRACTION14.61TORSIONAL
12B6539X-RAY DIFFRACTION14.61TORSIONAL
13C6539X-RAY DIFFRACTION14.61TORSIONAL
14D6539X-RAY DIFFRACTION14.61TORSIONAL
15E6539X-RAY DIFFRACTION14.61TORSIONAL
16F6539X-RAY DIFFRACTION14.61TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1985-3.260.33141470.28161209135699
3.26-3.32640.29711410.26812571398100
3.3264-3.39860.32541160.250812671383100
3.3986-3.47760.29831440.242712161360100
3.4776-3.56440.33691330.254812711404100
3.5644-3.66060.30641560.238512051361100
3.6606-3.76810.3381320.24412711403100
3.7681-3.88940.30731490.239112201369100
3.8894-4.02810.28631480.221612671415100
4.0281-4.18890.2441350.196912471382100
4.1889-4.3790.21481310.200312981429100
4.379-4.6090.24321350.174112381373100
4.609-4.89650.24491130.177413001413100
4.8965-5.27240.21141450.168612781423100
5.2724-5.79920.26781470.21712731420100
5.7992-6.62960.28041460.248212851431100
6.6296-8.31990.2731700.240913011471100
8.3199-29.02530.24691590.21413921551100

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