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- PDB-4w7e: Crystal Structure of Full-Length Split GFP Mutant E124H/K126H Wit... -

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Basic information

Entry
Database: PDB / ID: 4w7e
TitleCrystal Structure of Full-Length Split GFP Mutant E124H/K126H With Copper Mediated Crystal Contacts, P 41 21 2 Space Group
Componentsfluorescent protein D21H/K26H
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / COPPER (II) ION / IMIDAZOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.592 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 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 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_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 / _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
Revision 1.6Nov 20, 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/K26H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2533
Polymers26,1201
Non-polymers1332
Water46826
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.050, 96.050, 69.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein fluorescent protein D21H/K26H


Mass: 26120.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Imidazole pH 8.0, 10% PEG8000

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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: Dec 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.592→67.92 Å / Num. obs: 10580 / % possible obs: 99.7 % / Redundancy: 12.8 % / Rsym value: 0.132 / Net I/σ(I): 19.81

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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: 2.592→67.92 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 1056 9.99 %
Rwork0.207 --
obs0.213 10574 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.592→67.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 6 26 1820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091842
X-RAY DIFFRACTIONf_angle_d1.2672491
X-RAY DIFFRACTIONf_dihedral_angle_d15.177679
X-RAY DIFFRACTIONf_chiral_restr0.044268
X-RAY DIFFRACTIONf_plane_restr0.006323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.592-2.71030.43881250.33671128X-RAY DIFFRACTION98
2.7103-2.85320.39821280.28351154X-RAY DIFFRACTION100
2.8532-3.03190.33741310.26571174X-RAY DIFFRACTION100
3.0319-3.2660.34171310.2071179X-RAY DIFFRACTION100
3.266-3.59470.29451320.20641184X-RAY DIFFRACTION100
3.5947-4.11480.22311310.191196X-RAY DIFFRACTION100
4.1148-5.18390.17611340.161205X-RAY DIFFRACTION100
5.1839-67.94090.26051440.21461298X-RAY DIFFRACTION100

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