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- PDB-5f9g: pnGFP1.5-Y.Cro: circularly permuted green fluorescent protein (wi... -

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Basic information

Entry
Database: PDB / ID: 5f9g
TitlepnGFP1.5-Y.Cro: circularly permuted green fluorescent protein (with a tyrosine-derived chromophore)
ComponentspnGFP1.5-Y.Cro,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / green fluorescent protein / circularly permuted
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: 2.772 Å
AuthorsRemington, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1351933 United States
CitationJournal: To Be Published
Title: pnGFP: circularly permuted green fluorescent protein
Authors: Remington, S.J.
History
DepositionDec 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / diffrn_radiation_wavelength / 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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pnGFP1.5-Y.Cro,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,9271
Polymers28,9271
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.258, 57.258, 185.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein pnGFP1.5-Y.Cro,Green fluorescent protein / circularly permuted green fluorescent protein


Mass: 28927.461 Da / Num. of mol.: 1 / Fragment: UNP residues 145-238, UNP residues 2-144 / Mutation: circular permutation,circular permutation
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: pnGFP1.5-Y.Cro in buffer 50mM Hepes pH 7.5, 0.3M NaCl, 1mM beta-mercaptoethanol, A280=52; Crystals were grown in drops of 1ul protein solution: 1ul well solution containing 20-22% PEG 3350, ...Details: pnGFP1.5-Y.Cro in buffer 50mM Hepes pH 7.5, 0.3M NaCl, 1mM beta-mercaptoethanol, A280=52; Crystals were grown in drops of 1ul protein solution: 1ul well solution containing 20-22% PEG 3350, 0.25M potassium thiocyanate, 0.1M Tris pH 8.0
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2014
Details: cryo:24% PEG 3350, .25M KSCN, .15M NaCl, 50mM Hepes 7.5 plus either 20% Ethylene glycol or 60% ethylene glycol and .8M NDSB-201
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 14821 / % possible obs: 99.8 % / Redundancy: 24.7 % / CC1/2: 0.968 / Rmerge(I) obs: 0.089 / Net I/σ(I): 80.4
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 27.1 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EMB

1emb


Resolution: 2.772→24.682 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2947 410 4.96 %Random selection
Rwork0.2028 ---
obs0.2075 8260 97.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.772→24.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1825 0 0 16 1841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011880
X-RAY DIFFRACTIONf_angle_d1.4422537
X-RAY DIFFRACTIONf_dihedral_angle_d17.38687
X-RAY DIFFRACTIONf_chiral_restr0.049274
X-RAY DIFFRACTIONf_plane_restr0.007331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7719-3.17220.33951280.24772493X-RAY DIFFRACTION96
3.1722-3.99390.3341280.24432582X-RAY DIFFRACTION98
3.9939-24.68310.27091540.17652775X-RAY DIFFRACTION99

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