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- PDB-8u0y: Bacterial protein cpx -

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Basic information

Entry
Database: PDB / ID: 8u0y
TitleBacterial protein cpx
Components
  • (Fluorescent protein) x 2
  • Receptor A
  • Receptor B
KeywordsLUMINESCENT PROTEIN / Bacterial protein / Bacterial light harvesting complex / Phycobilisome
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHYCOUROBILIN / TRAV4D-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Ceramium secundatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGully, B.S. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP230102073 Australia
CitationJournal: To Be Published
Title: Bacterial protein cpx
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 1.1Oct 16, 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
A: Fluorescent protein
B: Fluorescent protein
C: Receptor A
D: Receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5279
Polymers84,5744
Non-polymers2,9545
Water32418
1
A: Fluorescent protein
B: Fluorescent protein
C: Receptor A
D: Receptor B
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)525,16554
Polymers507,44324
Non-polymers17,72130
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
crystal symmetry operation10_775-y+2,-x+2,-z1
crystal symmetry operation11_755-x+y+2,y,-z1
crystal symmetry operation12_555x,x-y,-z1
Buried area101250 Å2
ΔGint-710 kcal/mol
Surface area185350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.790, 221.790, 139.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Fluorescent protein


Mass: 17775.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ceramium secundatum (eukaryote)
#2: Protein Fluorescent protein


Mass: 18352.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ceramium secundatum (eukaryote)
#3: Protein Receptor A


Mass: 21515.865 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: TRAV4D-4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5R1F7
#4: Protein Receptor B


Mass: 26929.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 23 molecules

#5: Chemical
ChemComp-PUB / PHYCOUROBILIN


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


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.93 Å3/Da / Density % sol: 79.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 1.2 M ammonium sulfate, 5% w/v D-sorbitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / 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: 3→96.04 Å / Num. obs: 40827 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 46.71 Å2 / CC1/2: 0.965 / Rpim(I) all: 0.114 / Net I/σ(I): 7.4
Reflection shellResolution: 3→3.16 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5859 / CC1/2: 0.407 / Rpim(I) all: 0.484 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EYX

1eyx


Resolution: 3→79.08 Å / SU ML: 0.3752 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.4629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2583 2052 5.03 %
Rwork0.2331 38756 -
obs0.2344 40808 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.08 Å2
Refinement stepCycle: LAST / Resolution: 3→79.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5665 0 215 18 5898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01196003
X-RAY DIFFRACTIONf_angle_d1.42248190
X-RAY DIFFRACTIONf_chiral_restr0.0627917
X-RAY DIFFRACTIONf_plane_restr0.00961053
X-RAY DIFFRACTIONf_dihedral_angle_d20.59522086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.34671380.30452524X-RAY DIFFRACTION100
3.07-3.150.32241360.29832535X-RAY DIFFRACTION100
3.15-3.230.33181320.27812554X-RAY DIFFRACTION100
3.23-3.330.30681130.26562555X-RAY DIFFRACTION100
3.33-3.430.27881170.2662574X-RAY DIFFRACTION100
3.43-3.560.28331440.24742543X-RAY DIFFRACTION100
3.56-3.70.30541280.25252562X-RAY DIFFRACTION99.56
3.7-3.870.25811210.22292573X-RAY DIFFRACTION100
3.87-4.070.22521310.21632555X-RAY DIFFRACTION99.89
4.07-4.330.25561400.19982567X-RAY DIFFRACTION99.93
4.33-4.660.22381590.18632566X-RAY DIFFRACTION99.74
4.66-5.130.24071400.2072600X-RAY DIFFRACTION99.89
5.13-5.870.25381580.22772598X-RAY DIFFRACTION99.96
5.87-7.40.26811320.24752665X-RAY DIFFRACTION99.64
7.4-79.080.19961630.21932785X-RAY DIFFRACTION99.16

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