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- PDB-4zf3: Crystal structure of Green Fluorescent Protein (GFP); S65T, H148D... -

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Basic information

Entry
Database: PDB / ID: 4zf3
TitleCrystal structure of Green Fluorescent Protein (GFP); S65T, H148D; circular permutant ( 50-51)
ComponentsGreen fluorescent protein
KeywordsFLUORESCENT PROTEIN
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 / Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsOltrogge, L.M. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM27738 United States
CitationJournal: Acs Cent.Sci. / Year: 2015
Title: Short Hydrogen Bonds and Proton Delocalization in Green Fluorescent Protein (GFP).
Authors: Oltrogge, L.M. / Boxer, S.G.
History
DepositionApr 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_radiation_wavelength / diffrn_source
Item: _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn
Item: _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 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 / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 1.6Nov 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)56,3532
Polymers56,3532
Non-polymers00
Water46826
1
A: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,1761
Polymers28,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)28,1761
Polymers28,1761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.370, 68.260, 57.870
Angle α, β, γ (deg.)90.000, 102.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Green fluorescent protein /


Mass: 28176.395 Da / Num. of mol.: 2
Mutation: S30R, Y39I, C48S, F64L, S65T, Q80R, F99S, N105K, E111V, I128Y, Y145F, H148D, M153T, K156N, V163A, K166T, I167V, I171V, S205T, A206V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P42212, UniProt: A0A059PIQ0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM sodium acetate, 100 mM NaCl, 5% (wt/vol) PEG 3550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2014
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.8 Å / Num. obs: 27729 / % possible obs: 99.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.87 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALAdata scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DUF

2duf


Resolution: 1.9→34.309 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 1390 5.03 %
Rwork0.2153 26267 -
obs0.2176 27657 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.56 Å2 / Biso mean: 37.8076 Å2 / Biso min: 14.98 Å2
Refinement stepCycle: final / Resolution: 1.9→34.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3388 0 0 26 3414
Biso mean---28.75 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083460
X-RAY DIFFRACTIONf_angle_d1.1474680
X-RAY DIFFRACTIONf_chiral_restr0.043530
X-RAY DIFFRACTIONf_plane_restr0.005600
X-RAY DIFFRACTIONf_dihedral_angle_d15.1191227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.96790.37081400.269626262766100
1.9679-2.04670.30381540.241625892743100
2.0467-2.13980.25261300.227226772807100
2.1398-2.25260.29411390.22662604274399
2.2526-2.39370.30641430.234726322775100
2.3937-2.57850.31731380.224826512789100
2.5785-2.83790.27971300.22926342764100
2.8379-3.24830.2241220.21826712793100
3.2483-4.09140.24831260.19692589271597
4.0914-34.31420.23871680.20292594276297

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