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- PDB-6dq1: sfGFP N149 mutated to 4-nitro-L-phenylalanine -

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Basic information

Entry
Database: PDB / ID: 6dq1
TitlesfGFP N149 mutated to 4-nitro-L-phenylalanine
ComponentssfGFP
KeywordsFLUORESCENT PROTEIN / super folder GFP / 4-nitro-L-phenylalanine / unnatural amino acid
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: 1.598 Å
AuthorsPhillips-Piro, C.M. / Savidge, N. / Lee, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1053946 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine.
Authors: Maurici, N. / Savidge, N. / Lee, B.U. / Brewer, S.H. / Phillips-Piro, C.M.
History
DepositionJun 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
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_2 / _pdbx_validate_close_contact.auth_atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sfGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9992
Polymers26,9761
Non-polymers231
Water4,900272
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: sfGFP
hetero molecules

A: sfGFP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9994
Polymers53,9532
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area3170 Å2
ΔGint-33 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.302, 55.302, 166.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-614-

HOH

21A-623-

HOH

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Components

#1: Protein sfGFP


Mass: 26976.396 Da / Num. of mol.: 1 / Mutation: N149 mutated to 4-nitro-L-phenylalanine
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1200 mM Malic Acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.598→50 Å / Num. obs: 35157 / % possible obs: 99.4 % / Redundancy: 13.9 % / CC1/2: 0.993 / Net I/σ(I): 36.83
Reflection shellResolution: 1.598→1.63 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.33 / Num. unique obs: 1706 / CC1/2: 0.82 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER(in Phenix)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.598→46.067 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1767 5.04 %Random selection
Rwork0.1605 ---
obs0.162 35063 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.598→46.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 1 272 2138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091983
X-RAY DIFFRACTIONf_angle_d1.0052692
X-RAY DIFFRACTIONf_dihedral_angle_d18.0441190
X-RAY DIFFRACTIONf_chiral_restr0.066288
X-RAY DIFFRACTIONf_plane_restr0.006382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5981-1.64130.25161240.22372482X-RAY DIFFRACTION98
1.6413-1.68960.26181330.20382500X-RAY DIFFRACTION99
1.6896-1.74420.21771400.18352494X-RAY DIFFRACTION99
1.7442-1.80650.21581290.1752497X-RAY DIFFRACTION99
1.8065-1.87890.19921320.16482515X-RAY DIFFRACTION99
1.8789-1.96440.23791500.21582537X-RAY DIFFRACTION99
1.9644-2.06790.2141210.16452539X-RAY DIFFRACTION100
2.0679-2.19750.16591090.1512578X-RAY DIFFRACTION100
2.1975-2.36720.21581180.18952528X-RAY DIFFRACTION98
2.3672-2.60540.18941390.15252577X-RAY DIFFRACTION100
2.6054-2.98230.21461610.16672585X-RAY DIFFRACTION100
2.9823-3.75710.17091560.14272643X-RAY DIFFRACTION100
3.7571-46.08650.1641550.1452821X-RAY DIFFRACTION100

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