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- PDB-6b7r: Truncated strand 11-less green fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 6b7r
TitleTruncated strand 11-less green fluorescent protein
ComponentsGreen 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: 1.73 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Green fluorescent protein
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5586
Polymers52,7292
Non-polymers8294
Water6,593366
1
B: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7793
Polymers26,3641
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7793
Polymers26,3641
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.548, 55.548, 139.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Green fluorescent protein /


Mass: 26364.439 Da / Num. of mol.: 2
Mutation: S30R, Y39I, C48S, F64L, S66X, Y66X, G66X, C70A, Q80R, F99S, N105K, E111V, I128T, Y145F, M153T, V163A, K166T, I167V, I171V, A206K
Source method: isolated from a genetically manipulated source
Details: Truncated protein missing beta strand 11 / Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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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: 2.12 Å3/Da / Density % sol: 41.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M CHES pH 9.5, 1.0M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.22 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.22 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 44426 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.039 / Rrim(I) all: 0.106 / Χ2: 2.236 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.796.91.05344160.7680.4321.1391.226100
1.79-1.867.20.744340.8880.2810.7541.37100
1.86-1.957.30.48444220.9410.1930.5211.553100
1.95-2.057.40.34344200.9640.1360.371.793100
2.05-2.187.40.25744540.9770.1020.2772.091100
2.18-2.357.40.19844390.9890.0780.2132.314100
2.35-2.587.40.15544260.990.0610.1672.51100
2.58-2.967.40.1144580.9950.0440.1192.92100
2.96-3.737.20.06744640.9980.0270.0723.48100
3.73-507.30.04744930.9980.0180.052.99799.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B3P

2b3p


Resolution: 1.73→29.602 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.86
RfactorNum. reflection% reflection
Rfree0.1839 2159 4.87 %
Rwork0.1579 --
obs0.1592 44338 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 67.2 Å2 / Biso mean: 26.4964 Å2 / Biso min: 13.04 Å2
Refinement stepCycle: final / Resolution: 1.73→29.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3571 0 52 366 3989
Biso mean--38.91 36.75 -
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073733
X-RAY DIFFRACTIONf_angle_d0.8515038
X-RAY DIFFRACTIONf_chiral_restr0.06540
X-RAY DIFFRACTIONf_plane_restr0.006642
X-RAY DIFFRACTIONf_dihedral_angle_d15.4452169
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7244-1.76450.36951290.29422692282196
1.7645-1.80870.3121310.240928302961100
1.8087-1.85760.2391560.201928082964100
1.8576-1.91220.23481450.171328482993100
1.9122-1.97390.19691400.163527782918100
1.9739-2.04450.19431660.157827752941100
2.0445-2.12630.19791270.162228642991100
2.1263-2.2230.16331520.147928122964100
2.223-2.34020.19261180.153628312949100
2.3402-2.48670.19061370.156428192956100
2.4867-2.67860.19551490.160628152964100
2.6786-2.9480.19491220.155528602982100
2.948-3.3740.1531660.148827832949100
3.374-4.24890.14841780.134428062984100
4.2489-29.60660.18661430.156528583001100
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)
11.32650.2371-0.25631.365-0.72611.6017-0.0324-0.038-0.0409-0.09930.05990.08130.0992-0.0138-0.0260.1709-0.0138-0.01370.1235-0.00870.1217-25.2499-26.85727.6363
21.32370.1678-0.72441.3755-0.20621.50430.0526-0.11660.1261-0.0563-0.0282-0.0482-0.02120.1052-0.01270.1181-0.0144-0.00610.1708-0.01730.1309-0.9195-2.534628.0847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'B' and resid -21 through 208)B-21 - 208
2X-RAY DIFFRACTION2(chain 'A' and resid -21 through 208)A-21 - 208

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