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- PDB-4w6t: Crystal Structure of Full-Length Split GFP Mutant E115H/T118H Wit... -

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Basic information

Entry
Database: PDB / ID: 4w6t
TitleCrystal Structure of Full-Length Split GFP Mutant E115H/T118H With Copper Mediated Crystal Contacts, P 43 21 2 Space Group
Componentsfluorescent protein E115H/T118H
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / BROMIDE ION / COPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsLeibly, D.J. / Waldo, G.S. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098177 United States
CitationJournal: Structure / Year: 2015
Title: A Suite of Engineered GFP Molecules for Oligomeric Scaffolding.
Authors: Leibly, D.J. / Arbing, M.A. / Pashkov, I. / DeVore, N. / Waldo, G.S. / Terwilliger, T.C. / Yeates, T.O.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
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
Revision 1.6Nov 6, 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: fluorescent protein E115H/T118H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,99215
Polymers26,1021
Non-polymers89014
Water2,864159
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.300, 105.300, 69.610
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 fluorescent protein E115H/T118H


Mass: 26102.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 3.7 Å3/Da / Density % sol: 66.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.15M Kbr, 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.604→74.46 Å / Num. obs: 51580 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rsym value: 0.07155 / Net I/σ(I): 17.81

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Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE: DEV_1555) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.604→74.46 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 5157 10 %
Rwork0.18 --
obs0.182 51563 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.604→74.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1830 0 47 159 2036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191949
X-RAY DIFFRACTIONf_angle_d1.7582621
X-RAY DIFFRACTIONf_dihedral_angle_d13.909727
X-RAY DIFFRACTIONf_chiral_restr0.106278
X-RAY DIFFRACTIONf_plane_restr0.009339
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.604-1.62220.30391580.27411436X-RAY DIFFRACTION94
1.6222-1.64130.3081680.25741509X-RAY DIFFRACTION100
1.6413-1.66140.25411710.24751538X-RAY DIFFRACTION100
1.6614-1.68240.26471680.2331511X-RAY DIFFRACTION100
1.6824-1.70450.26741690.22741520X-RAY DIFFRACTION100
1.7045-1.72790.24161720.22221543X-RAY DIFFRACTION100
1.7279-1.75260.24981700.20691532X-RAY DIFFRACTION100
1.7526-1.77870.23531700.20321527X-RAY DIFFRACTION100
1.7787-1.80650.21881690.19641517X-RAY DIFFRACTION100
1.8065-1.83610.26461700.19581537X-RAY DIFFRACTION100
1.8361-1.86780.20371690.19391517X-RAY DIFFRACTION100
1.8678-1.90180.21931710.19161539X-RAY DIFFRACTION100
1.9018-1.93840.21551720.19381544X-RAY DIFFRACTION100
1.9384-1.97790.22061690.18471529X-RAY DIFFRACTION100
1.9779-2.02090.22221700.18911521X-RAY DIFFRACTION100
2.0209-2.06790.2251730.19051560X-RAY DIFFRACTION100
2.0679-2.11970.20791700.1821533X-RAY DIFFRACTION100
2.1197-2.1770.21811730.19091552X-RAY DIFFRACTION100
2.177-2.2410.21271710.1831538X-RAY DIFFRACTION100
2.241-2.31340.22241720.19381546X-RAY DIFFRACTION100
2.3134-2.39610.22821720.18611548X-RAY DIFFRACTION100
2.3961-2.4920.22841730.19181558X-RAY DIFFRACTION100
2.492-2.60540.21661720.18791553X-RAY DIFFRACTION100
2.6054-2.74280.21421730.18391554X-RAY DIFFRACTION100
2.7428-2.91470.22851750.19311571X-RAY DIFFRACTION100
2.9147-3.13970.21641740.18811569X-RAY DIFFRACTION100
3.1397-3.45570.22931750.19661572X-RAY DIFFRACTION100
3.4557-3.95570.20971770.17511600X-RAY DIFFRACTION100
3.9557-4.98360.15941800.13771619X-RAY DIFFRACTION100
4.9836-74.53870.16191910.15241713X-RAY DIFFRACTION100

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