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- PDB-4w7a: Crystal Structure of Full-Length Split GFP Mutant D21H/K26C Disul... -

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Basic information

Entry
Database: PDB / ID: 4w7a
TitleCrystal Structure of Full-Length Split GFP Mutant D21H/K26C Disulfide and Metal-Mediated Dimer, P 21 21 21 Space Group, Form 4
Componentsfluorescent protein D21H/K26C
KeywordsFLUORESCENT PROTEIN / fluorescent protei
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: 3.603 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 / 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 23, 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)104,5327
Polymers104,3424
Non-polymers1913
Water00
1
A: fluorescent protein D21H/K26C
B: fluorescent protein D21H/K26C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2984
Polymers52,1712
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-22 kcal/mol
Surface area20930 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 area910 Å2
ΔGint-17 kcal/mol
Surface area21490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.830, 121.330, 192.560
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.: 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.: 3 / 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: 7.05 Å3/Da / Density % sol: 82.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 3M NaCl, 0.1M Bis-Tris pH 5.5

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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: Oct 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.603→96.28 Å / Num. obs: 33244 / % possible obs: 99.4 % / Redundancy: 6.6 % / Rsym value: 0.1225 / Net I/σ(I): 13.95

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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: 3.603→96.28 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3018 3325 10 %
Rwork0.278 --
obs0.2804 33234 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.603→96.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7082 0 3 0 7085
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117268
X-RAY DIFFRACTIONf_angle_d1.229815
X-RAY DIFFRACTIONf_dihedral_angle_d12.4092677
X-RAY DIFFRACTIONf_chiral_restr0.0611066
X-RAY DIFFRACTIONf_plane_restr0.0061265
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6026-3.65410.33011230.35231103X-RAY DIFFRACTION89
3.6541-3.70860.3231370.32491233X-RAY DIFFRACTION100
3.7086-3.76660.33261370.30241237X-RAY DIFFRACTION100
3.7666-3.82830.31341360.3091224X-RAY DIFFRACTION100
3.8283-3.89430.32181380.2781239X-RAY DIFFRACTION100
3.8943-3.96510.31731360.27711228X-RAY DIFFRACTION100
3.9651-4.04140.34081400.27941259X-RAY DIFFRACTION100
4.0414-4.12390.28541360.28291220X-RAY DIFFRACTION100
4.1239-4.21360.27481380.28071244X-RAY DIFFRACTION100
4.2136-4.31160.26641390.26031247X-RAY DIFFRACTION100
4.3116-4.41940.28671350.25041219X-RAY DIFFRACTION100
4.4194-4.53890.26211390.23641245X-RAY DIFFRACTION100
4.5389-4.67250.25391380.21911247X-RAY DIFFRACTION99
4.6725-4.82330.24911380.21491240X-RAY DIFFRACTION100
4.8233-4.99570.25071370.21641231X-RAY DIFFRACTION100
4.9957-5.19570.24761400.22931262X-RAY DIFFRACTION100
5.1957-5.43210.31511390.26091252X-RAY DIFFRACTION100
5.4321-5.71850.31331410.27991264X-RAY DIFFRACTION100
5.7185-6.07670.33351380.32041250X-RAY DIFFRACTION100
6.0767-6.54580.36411400.31661260X-RAY DIFFRACTION100
6.5458-7.20430.32311410.30781268X-RAY DIFFRACTION99
7.2043-8.24630.33171430.31471281X-RAY DIFFRACTION100
8.2463-10.38750.27511440.24991300X-RAY DIFFRACTION100
10.3875-96.31440.34111520.33561356X-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)
10.05080.0411-0.01840.1349-0.10140.102-0.0409-0.04150.0263-0.1679-0.0915-0.02790.02270.0823-0.1490.5125-0.02350.0468-0.05720.06520.34216.2618-8.9473-42.5719
20.34680.08020.14450.02980.02480.13510.2075-0.12470.0836-0.2336-0.0033-0.04210.2081-0.0290.04490.74530.11540.09010.2898-0.03910.49117.7124-44.9772-44.2849
30.04410.0821-0.02280.136-0.04750.10220.031-0.2493-0.0821-0.0543-0.1261-0.1486-0.13770.3415-0.26910.0032-0.19920.13760.707-0.1130.26880.0886-25.7378-6.9484
40.0515-0.00360.09230.07770.00540.138-0.02960.00020.2221-0.0103-0.06460.0160.2042-0.3196-00.5744-0.0245-0.17611.206-0.10380.678236.2702-28.1099-8.7036
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 4:230)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 4:229)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 4:230)
4X-RAY DIFFRACTION4(CHAIN D AND RESSEQ 4:230)

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