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- PDB-4w6d: Crystal Structure of Full-Length Split GFP Mutant K26C Disulfide ... -

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Basic information

Entry
Database: PDB / ID: 4w6d
TitleCrystal Structure of Full-Length Split GFP Mutant K26C Disulfide Dimer, P 32 2 1 Space Group, Form 1
Componentsfluorescent protein K26CFluorescence
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: 3.45 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.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

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Assembly

Deposited unit
A: fluorescent protein K26C
B: fluorescent protein K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6293
Polymers53,6042
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-15 kcal/mol
Surface area21590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.110, 123.110, 151.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein fluorescent protein K26C / Fluorescence


Mass: 26802.102 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)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 6.18 Å3/Da / Density % sol: 80.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75 / Details: 1.5M MgSO4, 0.5% Glycerol, 0.1M MES pH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.447→87.16 Å / Num. obs: 17869 / % possible obs: 99.26 % / Redundancy: 5 % / Rsym value: 0.1177 / Net I/σ(I): 11.91

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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: PDB entry 2B3P

2b3p


Resolution: 3.45→87.16 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.267 1787 10.01 %
Rwork0.236 --
obs0.239 17861 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.45→87.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3549 0 1 0 3550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063662
X-RAY DIFFRACTIONf_angle_d1.4684950
X-RAY DIFFRACTIONf_dihedral_angle_d13.9451354
X-RAY DIFFRACTIONf_chiral_restr0.055540
X-RAY DIFFRACTIONf_plane_restr0.006639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.447-3.53970.30561350.32171215X-RAY DIFFRACTION98
3.5397-3.64390.31581330.28631200X-RAY DIFFRACTION100
3.6439-3.76150.26451370.27891236X-RAY DIFFRACTION100
3.7615-3.89590.28541370.27221227X-RAY DIFFRACTION100
3.8959-4.05190.27941340.26691207X-RAY DIFFRACTION99
4.0519-4.23630.26511370.23531236X-RAY DIFFRACTION99
4.2363-4.45970.26621350.20651210X-RAY DIFFRACTION100
4.4597-4.7390.2411400.20081263X-RAY DIFFRACTION100
4.739-5.10490.23781360.2051217X-RAY DIFFRACTION99
5.1049-5.61860.24141380.21541245X-RAY DIFFRACTION99
5.6186-6.43140.32191380.25281242X-RAY DIFFRACTION100
6.4314-8.10190.29561400.26681257X-RAY DIFFRACTION99
8.1019-87.18360.24371470.2181319X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 52.3418 Å / Origin y: 5.1632 Å / Origin z: -35.0181 Å
111213212223313233
T1.1996 Å20.1519 Å2-0.0356 Å2-0.7066 Å20.0014 Å2--0.7749 Å2
L1.7408 °2-1.4754 °2-0.1406 °2-3.5155 °20.4729 °2--1.4782 °2
S-0.2294 Å °-0.245 Å °-0.0999 Å °0.518 Å °0.1993 Å °0.2118 Å °0.2042 Å °-0.3604 Å °0.0017 Å °
Refinement TLS groupSelection details: ALL

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