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Entry
Database: PDB / ID: 6ofk
TitleCrystal structure of green fluorescent protein (GFP); S65T; ih circular permutant (50-51)
ComponentsGreen Fluorescent Protein (GFP); S65T; ih circular permutant (50-51)
KeywordsFLUORESCENT PROTEIN / GFP
Function / homologyGreen fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / ACETATE ION / Green fluorescent protein
Function and homology information
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsLin, C.-Y. / Romei, M.G. / Mathews, I.I. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)118044 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins.
Authors: Lin, C.Y. / Romei, M.G. / Oltrogge, L.M. / Mathews, I.I. / Boxer, S.G.
History
DepositionMar 30, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Feb 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 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 (GFP); S65T; ih circular permutant (50-51)
B: Green Fluorescent Protein (GFP); S65T; ih circular permutant (50-51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2263
Polymers56,1672
Non-polymers591
Water7,242402
1
A: Green Fluorescent Protein (GFP); S65T; ih circular permutant (50-51)


Theoretical massNumber of molelcules
Total (without water)28,0831
Polymers28,0831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green Fluorescent Protein (GFP); S65T; ih circular permutant (50-51)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1422
Polymers28,0831
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.937, 68.887, 60.948
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 240
2010B1 - 240

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Components

#1: Protein Green Fluorescent Protein (GFP); S65T; ih circular permutant (50-51)


Mass: 28083.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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: 1.91 Å3/Da / Density % sol: 35.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.15 M ammonium acetate, 34% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.15→36.49 Å / Num. obs: 146731 / % possible obs: 98 % / Redundancy: 13.5 % / Biso Wilson estimate: 15.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.035 / Net I/σ(I): 28.4
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 14174 / CC1/2: 0.781 / Rrim(I) all: 1.76 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zf3

4zf3


Resolution: 1.15→36.49 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.659 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1776 7336 5 %RANDOM
Rwork0.14968 ---
obs0.15108 139384 98.09 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å20.18 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.15→36.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 48 402 4018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133913
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173583
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.6645353
X-RAY DIFFRACTIONr_angle_other_deg1.4631.5928402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21223.951205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96515683
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9551516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024434
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9092.041888
X-RAY DIFFRACTIONr_mcbond_other1.8832.0381886
X-RAY DIFFRACTIONr_mcangle_it2.3433.0672367
X-RAY DIFFRACTIONr_mcangle_other2.3433.0682368
X-RAY DIFFRACTIONr_scbond_it2.6632.3252025
X-RAY DIFFRACTIONr_scbond_other2.6622.3262026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2293.3792951
X-RAY DIFFRACTIONr_long_range_B_refined3.66725.0034246
X-RAY DIFFRACTIONr_long_range_B_other3.5424.3014139
X-RAY DIFFRACTIONr_rigid_bond_restr2.7637496
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7321 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.149→1.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 521 -
Rwork0.362 9893 -
obs--94.8 %

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