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- PDB-4w7x: Crystal Structure of Full-Length Split GFP Mutant E115C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w7x
TitleCrystal Structure of Full-Length Split GFP Mutant E115C Disulfide Dimer, P 1 21 1 Space Group
Componentsfluorescent protein E115C/T118H
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: fluorescent protein E115C/T118H
B: fluorescent protein E115C/T118H
C: fluorescent protein E115C/T118H
D: fluorescent protein E115C/T118H


Theoretical massNumber of molelcules
Total (without water)104,2704
Polymers104,2704
Non-polymers00
Water00
1
A: fluorescent protein E115C/T118H
B: fluorescent protein E115C/T118H


Theoretical massNumber of molelcules
Total (without water)52,1352
Polymers52,1352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: fluorescent protein E115C/T118H
D: fluorescent protein E115C/T118H


Theoretical massNumber of molelcules
Total (without water)52,1352
Polymers52,1352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.840, 70.470, 116.780
Angle α, β, γ (deg.)90.00, 92.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
fluorescent protein E115C/T118H


Mass: 26067.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
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: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.0 M (NH4)2HPO4, acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.8→66.77 Å / Num. obs: 26887 / % possible obs: 99.7 % / Redundancy: 6.8 % / Rsym value: 0.1897 / Net I/σ(I): 8.19

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1555)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.8→66.77 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.269 2688 10 %
Rwork0.217 --
obs0.223 26879 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→66.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7089 0 0 0 7089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047368
X-RAY DIFFRACTIONf_angle_d0.8649962
X-RAY DIFFRACTIONf_dihedral_angle_d15.3052736
X-RAY DIFFRACTIONf_chiral_restr0.031071
X-RAY DIFFRACTIONf_plane_restr0.0031292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.85080.40791390.32081250X-RAY DIFFRACTION100
2.8508-2.90570.37771420.3031281X-RAY DIFFRACTION100
2.9057-2.9650.32941380.29961236X-RAY DIFFRACTION100
2.965-3.02950.3851420.26741280X-RAY DIFFRACTION100
3.0295-3.09990.30911390.25641247X-RAY DIFFRACTION100
3.0999-3.17750.32161430.25141288X-RAY DIFFRACTION100
3.1775-3.26340.33821370.23041239X-RAY DIFFRACTION100
3.2634-3.35940.27461440.23491295X-RAY DIFFRACTION100
3.3594-3.46780.31271400.23291253X-RAY DIFFRACTION99
3.4678-3.59180.27791420.22061280X-RAY DIFFRACTION100
3.5918-3.73550.27061410.22611268X-RAY DIFFRACTION100
3.7355-3.90550.29931420.22321283X-RAY DIFFRACTION100
3.9055-4.11140.22921400.20541255X-RAY DIFFRACTION100
4.1114-4.3690.25731420.18481279X-RAY DIFFRACTION100
4.369-4.70620.22381430.18671285X-RAY DIFFRACTION99
4.7062-5.17970.20771390.17711267X-RAY DIFFRACTION100
5.1797-5.92880.22441430.21231288X-RAY DIFFRACTION100
5.9288-7.46810.33271440.21511293X-RAY DIFFRACTION99
7.4681-66.79230.22061480.20111324X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.14890.4153-0.07851.4804-0.25491.6058-0.04830.07140.10460.03090.01730.05830.0419-0.056400.30490.0168-0.01540.2941-0.00250.3233-46.7257-48.7104-62.6721
21.12740.37250.04721.17660.05411.23380.02610.0582-0.04650.0124-0.0140.01130.07070.0443-00.30850.00110.01620.3266-0.00160.3063-19.3208-34.1007-76.1657
32.8984-0.1777-0.37081.74040.11141.83690.0740.22340.1183-0.0893-0.0699-0.02140.1653-0.1075-0.02790.41220.03760.030.47190.03770.3107-3.9522-43.6422-103.0588
42.14640.0614-0.09192.5965-0.14073.73020.1133-0.0782-0.1518-0.057-0.09670.3425-0.187-0.20460.02180.4230.06710.01170.45620.04960.4124-6.9265-29.8395-134.1673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:229)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 3:228)
4X-RAY DIFFRACTION4(CHAIN D AND RESSEQ 4:228)

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