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- PDB-4w6c: Crystal Structure of Full-Length Split GFP Mutant K26C Disulfide ... -

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Basic information

Entry
Database: PDB / ID: 4w6c
TitleCrystal Structure of Full-Length Split GFP Mutant K26C Disulfide Dimer, P 21 21 21 Space Group
Componentsfluorescent protein D21H/K26C
KeywordsFLUORESCENT PROTEIN / dimer / disulfide
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: 2.4924 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 / 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 1.6Oct 23, 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 D21H/K26C
B: fluorescent protein D21H/K26C


Theoretical massNumber of molelcules
Total (without water)52,1712
Polymers52,1712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-7 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.330, 88.370, 120.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein fluorescent protein D21H/K26C


Mass: 26085.398 Da / Num. of mol.: 2
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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 35% MPD, 0.1M Imidazole pH 8.0, 0.2M MgCl2

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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: 2.49→71.3 Å / Num. obs: 19311 / % possible obs: 97.33 % / Redundancy: 4.2 % / Rsym value: 0.1036 / Net I/σ(I): 7.28

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 2.4924→71.3 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2761 1929 10.01 %
Rwork0.248 --
obs0.2506 19278 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4924→71.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 0 0 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123648
X-RAY DIFFRACTIONf_angle_d1.3664933
X-RAY DIFFRACTIONf_dihedral_angle_d16.2241349
X-RAY DIFFRACTIONf_chiral_restr0.071534
X-RAY DIFFRACTIONf_plane_restr0.008638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4924-2.55470.46331200.4281079X-RAY DIFFRACTION85
2.5547-2.62380.4021340.40771203X-RAY DIFFRACTION98
2.6238-2.7010.37961370.37971230X-RAY DIFFRACTION98
2.701-2.78820.36711360.3491220X-RAY DIFFRACTION98
2.7882-2.88790.38281350.34631223X-RAY DIFFRACTION97
2.8879-3.00350.35771350.35011212X-RAY DIFFRACTION96
3.0035-3.14020.33461370.29611232X-RAY DIFFRACTION99
3.1402-3.30570.31841380.27011248X-RAY DIFFRACTION98
3.3057-3.51280.32271380.2671242X-RAY DIFFRACTION99
3.5128-3.78410.26151410.24331261X-RAY DIFFRACTION98
3.7841-4.16480.21971390.21871251X-RAY DIFFRACTION98
4.1648-4.76740.22971420.18521278X-RAY DIFFRACTION99
4.7674-6.00590.26061430.21171292X-RAY DIFFRACTION99
6.0059-71.32950.24671540.22751378X-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)
12.65070.1987-0.20633.7837-0.99943.9788-0.18-0.15850.21330.42330.0619-0.5186-0.06120.09140.08460.37560.0304-0.09020.4146-0.04290.573117.82167.6885127.8905
23.30290.14910.37533.3879-0.75615.11990.10670.14230.30070.0915-0.0514-0.0668-0.84080.2805-0.06060.6368-0.0337-0.00180.45380.02920.465220.40457.2222165.8734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:227)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:229)

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