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- PDB-5wj4: Crystal structure of redox-sensitive green fluorescent protein Cl... -

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Basic information

Entry
Database: PDB / ID: 5wj4
TitleCrystal structure of redox-sensitive green fluorescent protein Clover mutant roClover1
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / clover / GFP / beta barrel
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: 1.631 Å
AuthorsLiu, C. / Campbell, B.C. / Petsko, G.A.
CitationJournal: Structure / Year: 2018
Title: Crystal Structure of Green Fluorescent Protein Clover and Design of Clover-Based Redox Sensors.
Authors: Campbell, B.C. / Petsko, G.A. / Liu, C.F.
History
DepositionJul 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jan 31, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _entity.pdbx_mutation / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct.title / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg
Revision 2.1Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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


Theoretical massNumber of molelcules
Total (without water)53,8692
Polymers53,8692
Non-polymers00
Water9,854547
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9341
Polymers26,9341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)26,9341
Polymers26,9341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)134.570, 134.570, 69.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Green fluorescent protein


Mass: 26934.385 Da / Num. of mol.: 2
Mutation: S30R, Y39N, S65X, Y65X, G65X, Q69A, F99S, N105T, Y145F, S147C, H148D, M153T, V163A, I171V, T203V, Q204C, E222Q.
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.87 Å3/Da / Density % sol: 57.13 % / Mosaicity: 0.34 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 100mM Tris, pH 8.5, 50mM MgCl2, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.63→39.19 Å / Num. obs: 79222 / % possible obs: 100 % / Redundancy: 14.6 % / Biso Wilson estimate: 24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.031 / Rrim(I) all: 0.117 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.63-1.66142.1150.3780.5842.19599.9
8.93-39.1912.10.0520.9970.0150.05498.8

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QYQ

1qyq


Resolution: 1.631→39.185 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.07
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 3971 5.02 %Random
Rwork0.1637 ---
obs0.1651 79118 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.09 Å2 / Biso mean: 32.1068 Å2 / Biso min: 14.4 Å2
Refinement stepCycle: final / Resolution: 1.631→39.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 0 547 4163
Biso mean---42.75 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163741
X-RAY DIFFRACTIONf_angle_d1.3655063
X-RAY DIFFRACTIONf_chiral_restr0.104548
X-RAY DIFFRACTIONf_plane_restr0.009664
X-RAY DIFFRACTIONf_dihedral_angle_d14.2512229
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.631-1.65090.34811300.318326432773
1.6509-1.67180.33661260.298726532779
1.6718-1.69380.28491350.278826492784
1.6938-1.7170.31921430.263626682811
1.717-1.74150.2821570.248526362793
1.7415-1.76750.22721620.221426212783
1.7675-1.79510.27231230.217526522775
1.7951-1.82460.21411360.192526782814
1.8246-1.8560.22431280.190626512779
1.856-1.88980.23681450.187526492794
1.8898-1.92610.23391500.18626472797
1.9261-1.96540.18281230.163626812804
1.9654-2.00820.17631430.159426612804
2.0082-2.05490.19381530.161626292782
2.0549-2.10630.22741550.164226692824
2.1063-2.16320.19691540.163326632817
2.1632-2.22690.20291320.153526822814
2.2269-2.29870.20291510.156926562807
2.2987-2.38090.19921370.155926942831
2.3809-2.47620.20271450.159326812826
2.4762-2.58890.17541230.157826922815
2.5889-2.72530.2061700.161326702840
2.7253-2.8960.19421370.16727062843
2.896-3.11950.17731320.1627332865
3.1195-3.43330.19271540.156627212875
3.4333-3.92970.18031250.153827432868
3.9297-4.94950.14981580.129827952953
4.9495-39.19660.17461440.158529243068
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3977-0.3384-0.07011.8519-0.2441.26470.0489-0.0925-0.12390.1919-0.05550.12280.05720.02870.00420.1835-0.0330.0310.18490.0030.1534-45.152936.37860.4195
23.3816-0.9818-0.24231.3237-0.07831.41580.07120.18080.0930.0112-0.0879-0.0661-0.0678-0.11790.0150.1327-0.0207-0.00830.22340.02260.1842-10.1925.7574-6.353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain 'A'A2 - 231
2X-RAY DIFFRACTION2Chain 'B'B2 - 231

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