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- PDB-6b7t: Truncated strand 10-less green fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 6b7t
TitleTruncated strand 10-less green fluorescent protein
ComponentsGreen fluorescent protein,Green fluorescent protein
KeywordsFLUORESCENT PROTEIN / Superfolder GFP / Truncated GFP / His-tag
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDeng, A. / Boxer, S.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM27738 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Insight into the Photochemistry of Split Green Fluorescent Proteins: A Unique Role for a His-Tag.
Authors: Deng, A. / Boxer, S.G.
History
DepositionOct 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 30, 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: Green fluorescent protein,Green fluorescent protein
B: Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)54,6732
Polymers54,6732
Non-polymers00
Water1,67593
1
A: Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,3371
Polymers27,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Green fluorescent protein,Green fluorescent protein


Theoretical massNumber of molelcules
Total (without water)27,3371
Polymers27,3371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.369, 67.212, 59.991
Angle α, β, γ (deg.)90.000, 98.810, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid -19 and (name N or name...
21(chain B and ((resid -19 and (name O or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISHISHIS(chain A and ((resid -19 and (name N or name...AA-195
12SERSERILEILE(chain A and ((resid -19 and (name N or name...AA-20 - 2184 - 237
13SERSERILEILE(chain A and ((resid -19 and (name N or name...AA-20 - 2184 - 237
14SERSERILEILE(chain A and ((resid -19 and (name N or name...AA-20 - 2184 - 237
21HISHISHISHIS(chain B and ((resid -19 and (name O or name...BB-195
22HISHISILEILE(chain B and ((resid -19 and (name O or name...BB-19 - 2185 - 237
23HISHISILEILE(chain B and ((resid -19 and (name O or name...BB-19 - 2185 - 237
24HISHISILEILE(chain B and ((resid -19 and (name O or name...BB-19 - 2185 - 237

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Components

#1: Protein Green fluorescent protein,Green fluorescent protein


Mass: 27336.527 Da / Num. of mol.: 2
Mutation: K3Q, S30R, Y39I, C48S, F64L, S66X, Y66X, G66X, C70A, Q80R, F99S, N105K, E111V, I128T, Y145F, M153T, V163A, K166T, I167V, I171V, L221H, F223Y, T225N,K3Q, S30R, Y39I, C48S, F64L, S66X, Y66X, ...Mutation: K3Q, S30R, Y39I, C48S, F64L, S66X, Y66X, G66X, C70A, Q80R, F99S, N105K, E111V, I128T, Y145F, M153T, V163A, K166T, I167V, I171V, L221H, F223Y, T225N,K3Q, S30R, Y39I, C48S, F64L, S66X, Y66X, G66X, C70A, Q80R, F99S, N105K, E111V, I128T, Y145F, M153T, V163A, K166T, I167V, I171V, L221H, F223Y, T225N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 1.8 Å3/Da / Density % sol: 31.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.0, 0.2M ammonium chloride, 22.5 v/v% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.69→35.12 Å / Num. obs: 42227 / % possible obs: 96.4 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Net I/σ(I): 10.2 / Num. measured all: 152607 / Scaling rejects: 43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.722.62.105365914290.1891.5742.6510.563.9
9.08-35.123.60.02810732950.9990.0170.03439.697.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.91→35.123 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1483 5 %
Rwork0.1791 28166 -
obs0.1806 29649 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.25 Å2 / Biso mean: 43.699 Å2 / Biso min: 16.2 Å2
Refinement stepCycle: final / Resolution: 1.91→35.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 0 93 3270
Biso mean---43.69 -
Num. residues----412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113270
X-RAY DIFFRACTIONf_angle_d1.1074430
X-RAY DIFFRACTIONf_chiral_restr0.073491
X-RAY DIFFRACTIONf_plane_restr0.008569
X-RAY DIFFRACTIONf_dihedral_angle_d16.941868
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1685X-RAY DIFFRACTION8.068TORSIONAL
12B1685X-RAY DIFFRACTION8.068TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.97170.33291340.26532549268398
1.9717-2.04210.26251340.2262534266897
2.0421-2.12390.23331330.20992530266399
2.1239-2.22050.24761350.18472580271599
2.2205-2.33760.21611350.18112549268498
2.3376-2.4840.23181310.17142492262396
2.484-2.67570.22691350.16572578271399
2.6757-2.94490.20571350.17222568270399
2.9449-3.37070.16491360.15992574271098
3.3707-4.24560.19831370.17022593273099
4.2456-35.12880.20281380.18322619275798
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)
12.11450.5095-0.54632.19651.09515.6242-0.06770.0399-0.02070.127-0.02160.00450.2839-0.07610.05680.2758-0.0016-0.03110.1519-0.00630.19748.54257.57341.6426
24.3046-0.7171-0.38633.8521-2.34247.31930.0769-0.36070.26890.27540.0021-0.1022-0.3810.4917-0.03530.2707-0.01070.00120.2445-0.05170.233511.076319.795527.2673
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid -20 through 218)A-20 - 218
2X-RAY DIFFRACTION2(chain 'B' and resid -19 through 218)B-19 - 218

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