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- PDB-4w6f: Crystal Structure of Full-Length Split GFP Mutant K26C Disulfide ... -

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Basic information

Entry
Database: PDB / ID: 4w6f
TitleCrystal Structure of Full-Length Split GFP Mutant K26C Disulfide Dimer, P 32 2 1 Space Group, Form 2
Componentsfluorescent protein D21H/K26C
KeywordsFLUORESCENT PROTEIN / dimer / disulfide
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / IMIDAZOLE / NICKEL (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.5Nov 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5067
Polymers52,1712
Non-polymers3355
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.980, 121.980, 140.090
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 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)
#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
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: 5.77 Å3/Da / Density % sol: 78.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 10% 2-propanol, 0.1M Imidazole pH 8.0, 5mM NiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→84.34 Å / Num. obs: 33538 / % possible obs: 100 % / Redundancy: 10 % / Rsym value: 0.3045 / Net I/σ(I): 5.64

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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: 2.7→84.34 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.238 3354 10 %
Rwork0.204 --
obs0.208 33533 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→84.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 21 0 3604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093710
X-RAY DIFFRACTIONf_angle_d1.3035009
X-RAY DIFFRACTIONf_dihedral_angle_d15.0721368
X-RAY DIFFRACTIONf_chiral_restr0.05541
X-RAY DIFFRACTIONf_plane_restr0.006648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.73980.27651350.23171217X-RAY DIFFRACTION99
2.7398-2.78070.27521410.22671265X-RAY DIFFRACTION100
2.7807-2.82410.29841350.23321223X-RAY DIFFRACTION100
2.8241-2.87040.26081360.21991223X-RAY DIFFRACTION100
2.8704-2.91990.26381390.21531248X-RAY DIFFRACTION100
2.9199-2.9730.27051400.21961256X-RAY DIFFRACTION100
2.973-3.03020.25361370.22731237X-RAY DIFFRACTION100
3.0302-3.09210.26611390.21281253X-RAY DIFFRACTION100
3.0921-3.15930.28161380.2271241X-RAY DIFFRACTION100
3.1593-3.23280.2771370.21061231X-RAY DIFFRACTION100
3.2328-3.31360.2421410.22171268X-RAY DIFFRACTION100
3.3136-3.40320.28031360.23461229X-RAY DIFFRACTION100
3.4032-3.50340.27961410.25331262X-RAY DIFFRACTION100
3.5034-3.61650.2831380.23511248X-RAY DIFFRACTION100
3.6165-3.74570.27131390.22681253X-RAY DIFFRACTION100
3.7457-3.89570.23311400.22731254X-RAY DIFFRACTION100
3.8957-4.0730.24281410.19361268X-RAY DIFFRACTION100
4.073-4.28770.21621390.17931250X-RAY DIFFRACTION100
4.2877-4.55630.21391400.17121261X-RAY DIFFRACTION100
4.5563-4.90810.20241420.15181276X-RAY DIFFRACTION100
4.9081-5.40190.18851410.15621269X-RAY DIFFRACTION100
5.4019-6.18340.19391430.19091289X-RAY DIFFRACTION100
6.1834-7.78960.22711440.21771294X-RAY DIFFRACTION100
7.7896-84.38620.23921520.22571364X-RAY DIFFRACTION100
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)
11.0028-0.0586-0.03213.1878-0.59181.893-0.2153-0.1518-0.06510.23310.26560.18540.2169-0.2089-0.010.63290.10030.04530.16380.04120.338260.9709-12.8116-30.452
21.5972-1.0649-0.36853.7355-0.04622.4827-0.11660.0438-0.4589-0.13960.0120.65010.3655-0.2894-0.0180.61870.23270.12610.44210.01460.548538.48919.3764-29.9579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 2:230)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:230)

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