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- PDB-4w69: Crystal Structure of Full-Length Split GFP Mutant Q157C Disulfide... -

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Basic information

Entry
Database: PDB / ID: 4w69
TitleCrystal Structure of Full-Length Split GFP Mutant Q157C Disulfide Dimer, P 43 21 2 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: 3.975 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 30, 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


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-4 kcal/mol
Surface area22570 Å2
Unit cell
Length a, b, c (Å)133.760, 133.760, 88.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.4M MgFormate, 0.1M Acetate pH 4.6, 2%w/v benzamidine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0717 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 3.975→94.58 Å / Num. obs: 7344 / % possible obs: 99.9 % / Redundancy: 15 % / Rsym value: 0.144 / Net I/σ(I): 16.94
Reflection shellResolution: 3.975→4.12 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.66 / Mean I/σ(I) obs: 2.1 / % possible all: 99.3

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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: 3.975→94.58 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 41.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.335 734 10.01 %
Rwork0.307 --
obs0.31 7334 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.975→94.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 0 0 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053584
X-RAY DIFFRACTIONf_angle_d0.9124841
X-RAY DIFFRACTIONf_dihedral_angle_d10.731330
X-RAY DIFFRACTIONf_chiral_restr0.036523
X-RAY DIFFRACTIONf_plane_restr0.004624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.975-4.28220.4321430.38361287X-RAY DIFFRACTION100
4.2822-4.71310.37541420.34791287X-RAY DIFFRACTION100
4.7131-5.3950.38031440.33491294X-RAY DIFFRACTION100
5.395-6.79690.37421480.36911330X-RAY DIFFRACTION100
6.7969-94.580.27871570.24661402X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.9249 Å / Origin y: 107.8372 Å / Origin z: 15.5278 Å
111213212223313233
T1.6084 Å20.0537 Å2-0.1964 Å2-1.7822 Å2-0.329 Å2--1.5482 Å2
L3.9193 °2-0.0944 °2-0.8695 °2--0.5154 °2-0.0514 °2---0.1156 °2
S-0.2664 Å °0.3802 Å °-0.0658 Å °0.111 Å °0.1037 Å °-0.026 Å °0.0358 Å °0.0773 Å °0.1402 Å °
Refinement TLS groupSelection details: ALL

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