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- PDB-8u0f: Bacterial fluorescent protein -

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Basic information

Entry
Database: PDB / ID: 8u0f
TitleBacterial fluorescent protein
Components
  • Bacterial fluorescent protein alpha
  • Bacterial fluorescent protein beta
KeywordsLUMINESCENT PROTEIN / Bacterial protein / Bacterial light harvesting complex / Phycobilisome
Function / homology
Function and homology information


phycobilisome / chloroplast thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
PHYCOCYANOBILIN / PHYCOUROBILIN / Phycoerythrin beta subunit / Phycoerythrin alpha subunit
Similarity search - Component
Biological speciesCeramium secundatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsGully, B.S. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102073 Australia
CitationJournal: To Be Published
Title: Bacterial fluorescent protein
Authors: Gully, B.S. / Rossjohn, J.
History
DepositionAug 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Bacterial fluorescent protein alpha
C: Bacterial fluorescent protein beta
K: Bacterial fluorescent protein alpha
L: Bacterial fluorescent protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,14914
Polymers72,2584
Non-polymers5,89110
Water5,080282
1
B: Bacterial fluorescent protein alpha
C: Bacterial fluorescent protein beta
hetero molecules

B: Bacterial fluorescent protein alpha
C: Bacterial fluorescent protein beta
hetero molecules

B: Bacterial fluorescent protein alpha
C: Bacterial fluorescent protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22321
Polymers108,3866
Non-polymers8,83615
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area29200 Å2
ΔGint-282 kcal/mol
Surface area41130 Å2
MethodPISA
2
K: Bacterial fluorescent protein alpha
L: Bacterial fluorescent protein beta
hetero molecules

K: Bacterial fluorescent protein alpha
L: Bacterial fluorescent protein beta
hetero molecules

K: Bacterial fluorescent protein alpha
L: Bacterial fluorescent protein beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22321
Polymers108,3866
Non-polymers8,83615
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area29170 Å2
ΔGint-283 kcal/mol
Surface area41010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)186.610, 186.610, 59.420
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETCYSCYSchain 'B'BA1 - 1641 - 164
121CYCCYCCYCCYCchain 'B'BE201
131CYCCYCCYCCYCchain 'B'BF202
241METMETCYSCYSchain 'K'KC1 - 1641 - 164
251CYCCYCCYCCYCchain 'K'KJ201
261CYCCYCCYCCYCchain 'K'KK202
172METMETILEILEchain 'C'CB1 - 1761 - 176
182PUBPUBPUBPUBchain 'C'CG201
192CYCCYCCYCCYCchain 'C'CH202
1102CYCCYCCYCCYCchain 'C'CI203
2112METMETILEILEchain 'L'LD1 - 1761 - 176
2122PUBPUBPUBPUBchain 'L'LL201
2132CYCCYCCYCCYCchain 'L'LM202
2142CYCCYCCYCCYCchain 'L'LN203

NCS ensembles :
ID
1
2

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Components

#1: Protein Bacterial fluorescent protein alpha


Mass: 17775.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceramium secundatum (eukaryote) / Gene: cpeA / Production host: Ceramium secundatum (eukaryote) / References: UniProt: Q1AH74
#2: Protein Bacterial fluorescent protein beta


Mass: 18352.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ceramium secundatum (eukaryote) / Gene: cpeB / Production host: Ceramium secundatum (eukaryote) / References: UniProt: Q1AH60
#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical ChemComp-PUB / PHYCOUROBILIN


Mass: 590.710 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H42N4O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.5, 1.2 M ammonium sulfate, 4% w/v benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.07→55.77 Å / Num. obs: 46942 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.67 Å2 / CC1/2: 0.964 / Rpim(I) all: 0.129 / Net I/σ(I): 6.9
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6827 / CC1/2: 0.209 / Rpim(I) all: 0.685 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.07→42.59 Å / SU ML: 0.2627 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.0704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 2404 5.13 %
Rwork0.1987 44442 -
obs0.2015 46846 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.71 Å2
Refinement stepCycle: LAST / Resolution: 2.07→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5466 0 0 282 5748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745560
X-RAY DIFFRACTIONf_angle_d1.32597572
X-RAY DIFFRACTIONf_chiral_restr0.0597824
X-RAY DIFFRACTIONf_plane_restr0.0062960
X-RAY DIFFRACTIONf_dihedral_angle_d21.29492128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.110.3121380.23732556X-RAY DIFFRACTION97.71
2.11-2.160.30371600.23042568X-RAY DIFFRACTION99.06
2.16-2.210.26851200.21872664X-RAY DIFFRACTION99.5
2.21-2.260.30651210.21672608X-RAY DIFFRACTION99.71
2.26-2.320.27131560.20682606X-RAY DIFFRACTION99.75
2.32-2.390.28171170.20742669X-RAY DIFFRACTION100
2.39-2.470.28781290.20322613X-RAY DIFFRACTION99.82
2.47-2.560.27781110.20712675X-RAY DIFFRACTION99.96
2.56-2.660.26091420.19782611X-RAY DIFFRACTION99.96
2.66-2.780.28311450.21682602X-RAY DIFFRACTION100
2.78-2.930.26521480.21242631X-RAY DIFFRACTION100
2.93-3.110.32331400.21422644X-RAY DIFFRACTION99.96
3.11-3.350.251700.20172565X-RAY DIFFRACTION99.96
3.35-3.690.24171670.18642615X-RAY DIFFRACTION99.89
3.69-4.220.19381580.16712590X-RAY DIFFRACTION100
4.22-5.320.19841480.16712620X-RAY DIFFRACTION100
5.32-42.590.22031340.20332605X-RAY DIFFRACTION98.85
Refinement TLS params.Method: refined / Origin x: 105.72861758 Å / Origin y: 188.741332289 Å / Origin z: 3.09195965396 Å
111213212223313233
T0.057671596972 Å2-0.029352686933 Å2-0.0077077641705 Å2-0.0287956490529 Å20.0042428166193 Å2--0.055921142254 Å2
L0.241823700586 °2-0.0446561406327 °2-0.0775727634536 °2-0.0573841825951 °20.0376507217545 °2--0.168364905961 °2
S-0.0346306869427 Å °0.0187172708871 Å °0.052605417032 Å °0.0357958806631 Å °0.0222951722424 Å °-0.0186253884028 Å °-0.040924007107 Å °0.0218246538556 Å °-0.00563504092788 Å °
Refinement TLS groupSelection details: all

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