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- PDB-8c7i: Crystal structure of the PS2 assembly factor Psb32 from the cyano... -

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Basic information

Entry
Database: PDB / ID: 8c7i
TitleCrystal structure of the PS2 assembly factor Psb32 from the cyanobactium Thermosyncechococcus vestitus (formerly elongatus)
ComponentsGreen fluorescent protein,Tll0404 protein
KeywordsSTRUCTURAL PROTEIN / Assembly Factor Photosystem 2 Cyanobacteria Membrane Protein Fusion Protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy / membrane
Similarity search - Function
TPM domain / TPM domain / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Green fluorescent protein / Tll0404 protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Thermosynechococcus vestitus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLiauw, P. / Gasper, R. / Nowaczyk, M.M. / Hofmann, E.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2341 Germany
German Research Foundation (DFG)FOR2092 Germany
German Research Foundation (DFG)SPP2002 Germany
Citation
Journal: To Be Published
Title: Cryo-EM analysis of a novel photosystem II assembly intermediate that binds Psb32
Authors: Bohn, S. / Lambertz, J. / Lo, Y.K. / Meier-Credo, J. / Fuertges, T. / Liauw, P. / Gasper, R. / Langer, J.D. / Hofmann, E. / Rudack, T. / Schuller, J. / Nowaczyk, M.M.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Cloning, expression, crystallization and preliminary X-ray studies of a superfolder GFP fusion of cyanobacterial Psb32.
Authors: Liauw, P. / Kannchen, D. / Gasper, R. / Dyczmons-Nowaczyk, N. / Nowaczyk, M.M. / Hofmann, E.
History
DepositionJan 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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

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Assembly

Deposited unit
A: Green fluorescent protein,Tll0404 protein


Theoretical massNumber of molelcules
Total (without water)48,6481
Polymers48,6481
Non-polymers00
Water28816
1
A: Green fluorescent protein,Tll0404 protein

A: Green fluorescent protein,Tll0404 protein


Theoretical massNumber of molelcules
Total (without water)97,2962
Polymers97,2962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area3710 Å2
ΔGint-13 kcal/mol
Surface area34720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.650, 145.650, 91.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Green fluorescent protein,Tll0404 protein


Mass: 48648.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Fusion of Psb32 with Superfolder GFP
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Thermosynechococcus vestitus (bacteria)
Gene: GFP, tll0404 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P42212, UniProt: Q8DLS4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1 M sodium citrate, 0.1 M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95107 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95107 Å / Relative weight: 1
ReflectionResolution: 2.12→47.68 Å / Num. obs: 1158546 / % possible obs: 99.3 % / Redundancy: 35.3 % / Biso Wilson estimate: 64.144 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.13 / Net I/σ(I): 24.87
Reflection shellResolution: 2.12→2.18 Å / Redundancy: 37.5 % / Rmerge(I) obs: 6.66 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 88765 / CC1/2: 0.563 / Rrim(I) all: 6.76 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIXdev_4788refinement
XDSVERSION Jan 10, 2022 BUILT=20220120data reduction
XSCALEVERSION Jan 10, 2022 BUILT=20220120data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→47.68 Å / SU ML: 0.3282 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3246
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 1639 5 %
Rwork0.2273 31139 -
obs0.2288 32778 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.8 Å2
Refinement stepCycle: LAST / Resolution: 2.12→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 0 16 3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00583250
X-RAY DIFFRACTIONf_angle_d0.79584410
X-RAY DIFFRACTIONf_chiral_restr0.0499488
X-RAY DIFFRACTIONf_plane_restr0.0068583
X-RAY DIFFRACTIONf_dihedral_angle_d15.6411195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.371330.34112527X-RAY DIFFRACTION98.01
2.18-2.250.35641330.31552518X-RAY DIFFRACTION98.62
2.25-2.330.3531320.31562547X-RAY DIFFRACTION99.11
2.33-2.430.35951340.29612539X-RAY DIFFRACTION98.63
2.43-2.540.31111340.27382556X-RAY DIFFRACTION99.41
2.54-2.670.32221350.26232550X-RAY DIFFRACTION99.15
2.67-2.840.27291360.27972581X-RAY DIFFRACTION99.34
2.84-3.060.32561370.29522594X-RAY DIFFRACTION99.35
3.06-3.360.30231360.25882597X-RAY DIFFRACTION99.64
3.37-3.850.27441390.2282634X-RAY DIFFRACTION99.6
3.85-4.850.20061410.16872670X-RAY DIFFRACTION99.89
4.85-47.680.22051490.20482826X-RAY DIFFRACTION99.93
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)
11.450165965760.260731745324-0.7702394337831.945864201220.4490358250561.836722897780.07769276683620.2947942064890.1793026620160.131520287935-0.1577117989380.0114390302938-1.12865194548-0.79027802852-0.07192859597961.113959284020.593064737567-0.1773672217820.995700372465-0.2706425916680.488449471137-44.97243.304-4.842
25.06974893219-0.100958025834-3.329698592343.12816000565-0.626217797982.353751983-0.03382889857070.9176423850930.168813752991-0.1579334532060.26805089319-0.6815582446990.3007316975980.442382001155-0.2853392504110.5613291321960.12785224866-0.1359301772450.753806266265-0.2543631219550.636887693107-28.08424.57-14.556
33.171262389040.5025385939620.6144094914690.568083107377-0.9434047739553.043639076030.43723404662-0.444293681076-1.076570354280.702206944934-0.598858968694-1.02948968534-0.3758105762510.5202585790440.1184457293740.78748897741-0.0485529633745-0.5268092121140.8161437848380.02742679061811.10761677149-8.79228.0948.041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -255:-27 )A-255 - -27
2X-RAY DIFFRACTION2( CHAIN A AND RESID -26:-1 )A-26 - -1
3X-RAY DIFFRACTION3( CHAIN A AND RESID 0:150 )A0 - 150

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