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- PDB-4w6a: Crystal Structure of Full-Length Split GFP Mutant Q157C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w6a
TitleCrystal Structure of Full-Length Split GFP Mutant Q157C Disulfide Dimer, P 32 2 1 Space Group
Componentsfluorescent protein Q157C
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: 2.991 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: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_validate_polymer_linkage
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.pdbx_dist_value / _struct_conn.pdbx_value_order / _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
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 Q157C
B: fluorescent protein Q157C


Theoretical massNumber of molelcules
Total (without water)53,6062
Polymers53,6062
Non-polymers00
Water00
1
A: fluorescent protein Q157C

A: fluorescent protein Q157C


Theoretical massNumber of molelcules
Total (without water)53,6062
Polymers53,6062
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
2
B: fluorescent protein Q157C


Theoretical massNumber of molelcules
Total (without water)26,8031
Polymers26,8031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.930, 88.930, 135.760
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 Q157C


Mass: 26803.152 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 2.0M NaFormate, 0.1M Na Acetate pH 4.6

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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: 2.991→77.02 Å / Num. obs: 12990 / % possible obs: 99.5 % / Redundancy: 19.4 % / Rsym value: 0.1626 / Net I/σ(I): 20.34

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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: 2.991→77.02 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 1301 10.02 %
Rwork0.191 --
obs0.196 12988 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.991→77.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3574 0 0 0 3574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123665
X-RAY DIFFRACTIONf_angle_d1.5764954
X-RAY DIFFRACTIONf_dihedral_angle_d15.0181361
X-RAY DIFFRACTIONf_chiral_restr0.085538
X-RAY DIFFRACTIONf_plane_restr0.007639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.991-3.11060.35941370.28431234X-RAY DIFFRACTION96
3.1106-3.25220.3021430.25981282X-RAY DIFFRACTION100
3.2522-3.42370.29031420.24041280X-RAY DIFFRACTION100
3.4237-3.63820.28091400.21921262X-RAY DIFFRACTION100
3.6382-3.91910.27271460.20331306X-RAY DIFFRACTION100
3.9191-4.31340.21911430.16991284X-RAY DIFFRACTION100
4.3134-4.93750.20421470.14941320X-RAY DIFFRACTION100
4.9375-6.22030.2061470.16781321X-RAY DIFFRACTION100
6.2203-77.04110.22231560.18751398X-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)
12.25020.05040.34054.66911.81643.54480.0299-0.00060.0933-0.2489-0.22330.4649-0.2457-0.35080.19880.59410.0735-0.01920.52540.00260.543229.867-1.776-14.2124
22.68480.1760.38023.45040.20682.67120.0488-0.0822-0.14520.1540.04770.08210.07670.2306-0.10490.54550.0658-0.03340.536-0.05120.561657.3607-8.0489-3.3695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 3:229)

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