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- PDB-4w7c: Crystal Structure of Full-Length Split GFP Mutant D21H/K26C Disul... -

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Basic information

Entry
Database: PDB / ID: 4w7c
TitleCrystal Structure of Full-Length Split GFP Mutant D21H/K26C Disulfide and Metal-Mediated Dimer, C 2 Space Group
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: 2.5 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 / 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_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 / _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 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: fluorescent protein D21H/K26C
B: fluorescent protein D21H/K26C
C: fluorescent protein D21H/K26C
D: fluorescent protein D21H/K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4696
Polymers104,3424
Non-polymers1272
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-18 kcal/mol
Surface area19950 Å2
MethodPISA
2
C: fluorescent protein D21H/K26C
D: fluorescent protein D21H/K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2343
Polymers52,1712
Non-polymers641
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-19 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)205.490, 69.420, 102.810
Angle α, β, γ (deg.)90.00, 110.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
fluorescent protein D21H/K26C


Mass: 26085.398 Da / Num. of mol.: 4
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.: 2 / 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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, 0.1M Cacodylate pH 6.5, 0.2M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 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: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→96.15 Å / Num. obs: 46757 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rsym value: 0.0733 / Net I/σ(I): 15.63

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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: 2.5→96.15 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2537 4648 10 %
Rwork0.2265 --
obs0.2292 46491 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→96.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7026 0 2 0 7028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147184
X-RAY DIFFRACTIONf_angle_d1.3369711
X-RAY DIFFRACTIONf_dihedral_angle_d15.8112652
X-RAY DIFFRACTIONf_chiral_restr0.0751052
X-RAY DIFFRACTIONf_plane_restr0.0051253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5005-2.52890.48031480.4341331X-RAY DIFFRACTION94
2.5289-2.55860.3941490.40771358X-RAY DIFFRACTION98
2.5586-2.58990.42941560.40191396X-RAY DIFFRACTION98
2.5899-2.62260.50341510.38451353X-RAY DIFFRACTION98
2.6226-2.65710.42371550.39581407X-RAY DIFFRACTION98
2.6571-2.69360.41041520.36181383X-RAY DIFFRACTION98
2.6936-2.7320.38621500.37531333X-RAY DIFFRACTION98
2.732-2.77280.37241590.34731428X-RAY DIFFRACTION99
2.7728-2.81610.36911480.33081340X-RAY DIFFRACTION97
2.8161-2.86230.35091570.3111405X-RAY DIFFRACTION98
2.8623-2.91170.35481540.30531376X-RAY DIFFRACTION99
2.9117-2.96460.34011550.29931395X-RAY DIFFRACTION99
2.9646-3.02170.36521580.31571433X-RAY DIFFRACTION99
3.0217-3.08330.2781490.28681346X-RAY DIFFRACTION99
3.0833-3.15040.32841580.25091414X-RAY DIFFRACTION99
3.1504-3.22370.28741540.24811373X-RAY DIFFRACTION99
3.2237-3.30430.29711570.24461411X-RAY DIFFRACTION99
3.3043-3.39360.28341540.22521399X-RAY DIFFRACTION99
3.3936-3.49350.25511560.23151411X-RAY DIFFRACTION99
3.4935-3.60630.27481550.24081398X-RAY DIFFRACTION99
3.6063-3.73520.23951540.21771381X-RAY DIFFRACTION97
3.7352-3.88470.26711560.2211412X-RAY DIFFRACTION99
3.8847-4.06150.24111560.21021395X-RAY DIFFRACTION99
4.0615-4.27570.2411570.18511414X-RAY DIFFRACTION100
4.2757-4.54350.18561560.1761411X-RAY DIFFRACTION99
4.5435-4.89430.18721580.1581414X-RAY DIFFRACTION99
4.8943-5.38680.16931580.17671421X-RAY DIFFRACTION98
5.3868-6.16620.27641540.21421393X-RAY DIFFRACTION99
6.1662-7.76820.2511620.21391458X-RAY DIFFRACTION100
7.7682-96.22510.18431620.20051454X-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)
16.51011.70380.93412.88310.44144.0046-0.2460.4161-0.10580.07930.394-0.2191-0.10510.5972-0.12550.6293-0.03930.02670.5067-0.1640.656241.314844.380635.5817
24.3859-0.1145-0.1382.1936-0.53915.68650.2496-0.143-0.50460.2678-0.11850.07750.4609-0.0236-0.15020.6352-0.0186-0.01120.5217-0.12740.68260.528556.161463.8784
33.79180.45430.30091.88240.29194.10640.2217-0.18180.230.2021-0.2198-0.0286-0.60480.54570.01940.7928-0.0783-0.0071.0499-0.15340.65984.85571.138873.1402
46.80211.07561.88492.29450.02096.01960.21171.1545-0.0703-0.1534-0.0466-0.1509-0.28651.2467-0.16370.7652-0.2383-0.04151.0637-0.15960.6849104.755379.1288102.1643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:229)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:229)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 4:228)
4X-RAY DIFFRACTION4(CHAIN D AND RESSEQ 6:227)

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