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- PDB-4w75: Crystal Structure of Full-Length Split GFP Mutant D21H/K26C Disul... -

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Basic information

Entry
Database: PDB / ID: 4w75
TitleCrystal Structure of Full-Length Split GFP Mutant D21H/K26C Disulfide and Metal-Mediated Dimer, P 21 21 21 Space Group, Form 1
Componentsfluorescent protein D21H/K26C
KeywordsFLUORESCENT PROTEIN
Function / homologyGreen Fluorescent Protein / Green fluorescent protein / Beta Barrel / Mainly Beta / COPPER (II) ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.473 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 1.0Mar 4, 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.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 D21H/K26C
B: fluorescent protein D21H/K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2343
Polymers52,1712
Non-polymers641
Water00
1
A: fluorescent protein D21H/K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1492
Polymers26,0851
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: fluorescent protein D21H/K26C


Theoretical massNumber of molelcules
Total (without water)26,0851
Polymers26,0851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-13 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 83.930, 121.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG MME 2000, 0.15M KBr

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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: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 3.473→69.13 Å / Num. obs: 8254 / % possible obs: 98.8 % / Redundancy: 12.7 % / Rsym value: 0.1496 / Net I/σ(I): 13.64

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 3.473→69.125 Å / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 43.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3446 817 9.99 %
Rwork0.3015 --
obs0.3057 8175 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.473→69.125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 1 0 3181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043247
X-RAY DIFFRACTIONf_angle_d0.8534375
X-RAY DIFFRACTIONf_dihedral_angle_d11.771180
X-RAY DIFFRACTIONf_chiral_restr0.054482
X-RAY DIFFRACTIONf_plane_restr0.003560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.473-3.69060.39881290.42571150X-RAY DIFFRACTION95
3.6906-3.97560.39871330.34611215X-RAY DIFFRACTION98
3.9756-4.37560.33391330.29691196X-RAY DIFFRACTION98
4.3756-5.00860.35071360.2841233X-RAY DIFFRACTION98
5.0086-6.30960.35031390.29181250X-RAY DIFFRACTION99
6.3096-69.13910.32081470.28741314X-RAY DIFFRACTION98
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)
15.35071.032-0.77456.42111.23535.80730.0252-0.3227-0.20190.45610.08380.06680.46430.5711-0.09871.43030.00760.05281.2115-0.03131.162215.58257.5788125.2347
24.3960.26282.6556.16540.25515.613-0.74620.58890.4869-0.3720.27430.2226-1.38880.23840.2141.51070.0275-0.09771.39730.18751.198812.23815.5425159.3546
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 13:227)

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