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- PDB-5bql: Fluorescent protein cyOFP -

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Basic information

Entry
Database: PDB / ID: 5bql
TitleFluorescent protein cyOFP
ComponentsFluorescent protein cyOFP
KeywordsFLUORESCENT PROTEIN
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
Fluorescent protein cyOFP
Similarity search - Component
Biological speciesEntacmaea quadricolor (sea anemone)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsSens, A. / Ataie, N. / Ng, H.L. / Lin, M.Z. / Chu, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1U01NS090600 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50GM107615 United States
CitationJournal: Sensors Basel Sensors / Year: 2016
Title: A Guide to Fluorescent Protein FRET Pairs.
Authors: Bajar, B.T. / Wang, E.S. / Zhang, S. / Lin, M.Z. / Chu, J.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 10, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen
Item: _entity.formula_weight / _entity_src_gen.gene_src_strain ..._entity.formula_weight / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fluorescent protein cyOFP
B: Fluorescent protein cyOFP
C: Fluorescent protein cyOFP
D: Fluorescent protein cyOFP


Theoretical massNumber of molelcules
Total (without water)110,0024
Polymers110,0024
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-36 kcal/mol
Surface area33300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.124, 102.764, 123.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fluorescent protein cyOFP


Mass: 27500.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entacmaea quadricolor (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A182DW87*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.29 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1M HEPES pH 7.5, 25% PEG 3350
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.01623 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01623 Å / Relative weight: 1
ReflectionResolution: 2.39→79 Å / Num. obs: 38045 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.53 % / Biso Wilson estimate: 58.76 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.092 / Χ2: 1.051 / Net I/σ(I): 14.8 / Num. measured all: 467689
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.39-2.530.6421.0221.946772711616112501.11496.8
2.53-2.710.8670.6143.467366510912108690.66599.6
2.71-2.930.9510.3575.76866710171101450.38799.7
2.93-3.20.9870.199.9263084940093860.20599.9
3.2-3.580.9960.09318.6856198846984600.10199.9
3.58-4.130.9980.06226.6948919748874850.067100
4.13-5.050.9980.04634.2440813632063190.05100
5.05-7.10.9980.04633.7530983490849070.05100
7.10.9990.03639.6917633277727590.03999.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 24.223 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.475 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 1858 4.9 %RANDOM
Rwork0.1925 ---
obs0.1955 35895 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.93 Å2 / Biso mean: 63.039 Å2 / Biso min: 32.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å2-0 Å2-0 Å2
2--0.14 Å2-0 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 2.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7139 0 1903 44 9086
Biso mean--69.92 50.41 -
Num. residues----653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197362
X-RAY DIFFRACTIONr_bond_other_d0.0020.026923
X-RAY DIFFRACTIONr_angle_refined_deg1.8261.9749921
X-RAY DIFFRACTIONr_angle_other_deg0.979316016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3485892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50724.214337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.613151267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3791537
X-RAY DIFFRACTIONr_chiral_restr0.0960.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218249
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021694
X-RAY DIFFRACTIONr_mcbond_it1.3813.6623565
X-RAY DIFFRACTIONr_mcbond_other1.3813.6623564
X-RAY DIFFRACTIONr_mcangle_it2.2055.4894446
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 143 -
Rwork0.333 2472 -
all-2615 -
obs--95.02 %
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)
13.58590.88890.22923.35280.85162.34140.3501-0.6322-0.05050.8555-0.11240.02780.4478-0.106-0.23770.3201-0.08020.04870.2811-0.13760.2182-17.7316-18.059939.2109
22.847-0.031-0.57313.09140.14312.23490.1850.32980.6301-0.34160.09490.7088-0.1624-0.4103-0.27990.0948-0.04870.03190.24970.00940.4116-24.7242-7.88310.9322
32.8235-0.4498-0.86281.88240.59282.21710.16650.34670.3288-0.2004-0.12250.016-0.11810.0701-0.0440.07210.01450.07710.06740.02780.13426.7547-2.27165.7309
42.05720.0419-0.10843.0417-0.59971.70620.0626-0.3574-0.14430.1253-0.10330.07460.03430.26410.04070.018-0.00660.03730.09770.02760.17712.9937-19.337230.8581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 232
2X-RAY DIFFRACTION2B7 - 232
3X-RAY DIFFRACTION3C7 - 231
4X-RAY DIFFRACTION4D8 - 231

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