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- PDB-3zpn: Structure of Psb28 -

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Basic information

Entry
Database: PDB / ID: 3zpn
TitleStructure of Psb28
ComponentsPHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II ASSEMBLY
Function / homology
Function and homology information


photosystem II oxygen evolving complex / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Photosystem II Psb28 / Photosystem II Psb28, class 1 / Photosystem II Psb28, class 1 superfamily / Psb28 protein / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Photosystem II assembly factor Psb28 protein
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.361 Å
AuthorsBialek, W.J. / Michoux, F. / Nixon, P.J. / Murray, J.W.
CitationJournal: Photosynth.Res. / Year: 2013
Title: Crystal Structure of the Psb28 Accessory Factor of Thermosynechococcus Elongatus Photosystem II at 2.3 A
Authors: Bialek, W. / Wen, S. / Michoux, F. / Beckova, M. / Komenda, J. / Murray, J.W. / Nixon, P.J.
History
DepositionFeb 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
B: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
C: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
D: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN


Theoretical massNumber of molelcules
Total (without water)60,3444
Polymers60,3444
Non-polymers00
Water95553
1
A: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
B: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1722
Polymers30,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-10 kcal/mol
Surface area11630 Å2
MethodPISA
2
C: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN
D: PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,1722
Polymers30,1722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-9.2 kcal/mol
Surface area11360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.060, 57.060, 183.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 4:108 )
211CHAIN B AND (RESSEQ 4:108 )
311CHAIN C AND (RESSEQ 4:108 )
411CHAIN D AND (RESSEQ 4:108 )

NCS oper:
IDCodeMatrixVector
1given(0.9836, -0.1795, -0.01884), (-0.1796, -0.9837, -0.003387), (-0.01793, 0.006715, -0.9998)-4.538, -50.2, 19.21
2given(0.9836, -0.1795, -0.01884), (-0.1796, -0.9837, -0.003387), (-0.01793, 0.006715, -0.9998)-4.538, -50.2, 19.21
3given(-0.5256, 0.5379, -0.6591), (-0.262, 0.6347, 0.7269), (0.8094, 0.5548, -0.1927)77.34, -1.947, 0.5218
4given(-0.5058, 0.3546, -0.7864), (0.3639, -0.7389, -0.5672), (-0.7822, -0.573, 0.2446)70.82, -63.88, 15.07

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Components

#1: Protein
PHOTOSYSTEM II REACTION CENTER PSB28 PROTEIN / PHOTOSYSTEM II 13 KDA PROTEIN / PHOTOSYSTEM II REACTION CENTER W PROTEIN


Mass: 15085.886 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): KRX / References: UniProt: Q8DLJ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.08 Å3/Da / Density % sol: 60.03 % / Description: NONE
Crystal growDetails: 35% W/V PEG 3350, 300MM POTASSIUM THIOCYANATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.36→57.06 Å / Num. obs: 23633 / % possible obs: 98.7 % / Observed criterion σ(I): 0 / Redundancy: 3.12 % / Biso Wilson estimate: 45.94 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.26
Reflection shellResolution: 2.36→2.42 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.52 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
TRUNCATEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KVO

2kvo


Resolution: 2.361→57.06 Å / SU ML: 0.35 / σ(F): 1.36 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2342 1195 5.1 %
Rwork0.1925 --
obs0.1945 23631 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.5 Å2
Refinement stepCycle: LAST / Resolution: 2.361→57.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 0 0 53 3466
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A844X-RAY DIFFRACTIONPOSITIONAL
12B844X-RAY DIFFRACTIONPOSITIONAL1.616
13C844X-RAY DIFFRACTIONPOSITIONAL1.848
14D844X-RAY DIFFRACTIONPOSITIONAL1.089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3614-2.4560.34291250.28662474X-RAY DIFFRACTION98
2.456-2.56780.35591250.26832503X-RAY DIFFRACTION100
2.5678-2.70310.30911370.25512511X-RAY DIFFRACTION99
2.7031-2.87250.31061560.23822490X-RAY DIFFRACTION100
2.8725-3.09430.27441520.22842473X-RAY DIFFRACTION99
3.0943-3.40560.24111220.20872478X-RAY DIFFRACTION98
3.4056-3.89830.19671360.1822481X-RAY DIFFRACTION99
3.8983-4.91110.21151260.15782517X-RAY DIFFRACTION99
4.9111-57.07660.17641160.15742509X-RAY DIFFRACTION97

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