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- PDB-5dph: sfGFP mutant - 149 p-cyano-L-phenylalanine -

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Basic information

Entry
Database: PDB / ID: 5dph
TitlesfGFP mutant - 149 p-cyano-L-phenylalanine
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN / GFP / unnatural amino acid / cyanophenylalanine
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
CARBON DIOXIDE / Green fluorescent protein / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsDippel, A.B. / Olenginski, G.M. / Maurici, N. / Liskov, M.T. / Brewer, S.H. / Phillips-Piro, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1053946 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study.
Authors: Dippel, A.B. / Olenginski, G.M. / Maurici, N. / Liskov, M.T. / Brewer, S.H. / Phillips-Piro, C.M.
History
DepositionSep 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.5Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,17111
Polymers53,9132
Non-polymers2589
Water10,215567
1
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1227
Polymers26,9561
Non-polymers1666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0494
Polymers26,9561
Non-polymers933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.270, 47.270, 344.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Green fluorescent protein /


Mass: 26956.408 Da / Num. of mol.: 2
Mutation: M1V, R2S, S30R, T65(CRO), Y66(CRO), G67(CRO), A72S, Q80R, A206V, N149(4CF)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: gfp / Plasmid: pBAD / Cell line (production host): DH10B / Production host: Escherichia coli (E. coli) / References: UniProt: A0A059PIQ0, UniProt: P42212*PLUS
#2: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 20% PEG 4000, 0.21 M MgCl2-6H2O / PH range: 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.42→57 Å / Num. obs: 81014 / % possible obs: 99.4 % / Redundancy: 36.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 45.1
Reflection shellResolution: 1.42→1.45 Å / Redundancy: 21.9 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.22 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.42→57 Å / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 26.76 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2078 4163 5.14 %Random selection
Rwork0.1798 ---
obs0.1832 81014 99.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.42→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 13 567 4230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113757
X-RAY DIFFRACTIONf_angle_d1.2455077
X-RAY DIFFRACTIONf_dihedral_angle_d15.0181373
X-RAY DIFFRACTIONf_chiral_restr0.067551
X-RAY DIFFRACTIONf_plane_restr0.005660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4205-1.4450.31822200.32983587X-RAY DIFFRACTION88
1.445-1.47130.35091890.31853779X-RAY DIFFRACTION92
1.4713-1.49960.32091980.30493753X-RAY DIFFRACTION94
1.4996-1.53020.30932080.31283898X-RAY DIFFRACTION95
1.5302-1.56350.30512130.2923855X-RAY DIFFRACTION95
1.5635-1.59980.28052240.29333816X-RAY DIFFRACTION94
1.5998-1.63980.30172320.28673888X-RAY DIFFRACTION94
1.6398-1.68420.2942020.27853849X-RAY DIFFRACTION95
1.6842-1.73370.2862210.27283839X-RAY DIFFRACTION95
1.7337-1.78960.26481760.27573890X-RAY DIFFRACTION96
1.7896-1.85360.26122060.25273821X-RAY DIFFRACTION94
1.8536-1.92770.24481870.2393874X-RAY DIFFRACTION95
1.9277-2.01540.24862330.23063837X-RAY DIFFRACTION94
2.0154-2.12160.21821980.22193891X-RAY DIFFRACTION95
2.1216-2.25440.21822140.20993875X-RAY DIFFRACTION95
2.2544-2.42830.21711970.19893837X-RAY DIFFRACTION95
2.4283-2.67230.20561920.1793893X-RAY DIFFRACTION95
2.6723-3.05830.20062330.15983840X-RAY DIFFRACTION94
3.0583-3.85010.1782120.12373866X-RAY DIFFRACTION95
3.8501-22.79550.14372040.11353895X-RAY DIFFRACTION95

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