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- PDB-4w77: Crystal Structure of Full-Length Split GFP Mutant D21H/K26C Disul... -

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Basic information

Entry
Database: PDB / ID: 4w77
TitleCrystal Structure of Full-Length Split GFP Mutant D21H/K26C Disulfide and Metal-Mediated Dimer, P 21 21 21 Space Group, Form 3
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: 3.1 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 18, 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 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 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 area840 Å2
ΔGint-18 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.120, 68.290, 121.580
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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 50% PEG200, 0.2M MgCl2, 0.1M NaCacodylate pH 6.5

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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: 3.1→60.79 Å / Num. obs: 9841 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rsym value: 0.1514 / Net I/σ(I): 9.86

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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: 3.1→60.79 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2908 984 10.01 %
Rwork0.2169 --
obs0.2243 9831 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→60.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3473 0 1 0 3474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113550
X-RAY DIFFRACTIONf_angle_d1.5194797
X-RAY DIFFRACTIONf_dihedral_angle_d15.7031301
X-RAY DIFFRACTIONf_chiral_restr0.075528
X-RAY DIFFRACTIONf_plane_restr0.006622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0999-3.26340.36871370.25271234X-RAY DIFFRACTION100
3.2634-3.46780.31921370.24091232X-RAY DIFFRACTION100
3.4678-3.73550.35121370.23331239X-RAY DIFFRACTION100
3.7355-4.11140.29221400.20041254X-RAY DIFFRACTION100
4.1114-4.70610.2471400.17961259X-RAY DIFFRACTION100
4.7061-5.92840.25331420.19471274X-RAY DIFFRACTION100
5.9284-60.80170.29721510.24711355X-RAY DIFFRACTION99
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)
14.4314-0.50860.66154.04210.78993.55860.14010.1090.0041-0.113-0.1630.2123-0.2204-0.30080.02550.38760.0802-0.01010.4861-0.02430.411-23.5065-2.31272.4135
22.56640.5398-0.43783.2169-0.02062.9635-0.0275-0.07470.17280.2756-0.08280.25090.06140.20530.07720.39770.01050.06410.43240.02970.4434-23.796-3.765-34.2766
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 5:227)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:227)

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