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- PDB-3ls0: Crystal Structure of Cyanobacterial PsbQ from Synechocystis sp. P... -

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Basic information

Entry
Database: PDB / ID: 3ls0
TitleCrystal Structure of Cyanobacterial PsbQ from Synechocystis sp. PCC 6803
ComponentsSll1638 protein
KeywordsPHOTOSYNTHESIS / Four helix bundle
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / photosynthesis / calcium ion binding
Similarity search - Function
Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 (PsbQ) / PsbQ-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJackson, S.A. / Fagerlund, R.D. / Wilbanks, S.M. / Eaton-Rye, J.J.
CitationJournal: Biochemistry / Year: 2010
Title: Crystal Structure of PsbQ from Synechocystis sp. PCC 6803 at 1.8 A: Implications for Binding and Function in Cyanobacterial Photosystem II
Authors: Jackson, S.A. / Fagerlund, R.D. / Wilbanks, S.M. / Eaton-Rye, J.J.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sll1638 protein


Theoretical massNumber of molelcules
Total (without water)14,6081
Polymers14,6081
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.332, 46.787, 93.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Sll1638 protein / PsbQ


Mass: 14608.493 Da / Num. of mol.: 1 / Fragment: residues 21-149
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: sll1638 / Plasmid: pGEX-6-P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P73048
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
12.1242.020
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2911vapor diffusion, hanging drop6.525% PEG 1450, 0.1M MES-NAOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
2912vapor diffusion, hanging drop725% PEG 1450, 0.05M MES, 0.05M TRIS-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.95364
SYNCHROTRONAustralian Synchrotron MX220.96064,0.97984
Detector
TypeIDDetectorDate
ADSC Omega 1801CCDAug 28, 2009
ADSC Omega 1802CCDAug 28, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.953641
20.960641
30.979841
ReflectionResolution: 1.8→19.13 Å / Num. all: 12135 / Num. obs: 12135 / % possible obs: 99.9 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible allRsym value
1.8-1.99.70.3955.8167941730100
1.9-2.0110.10.2283.41650416411000.228
2.01-2.15100.145.51536615361000.14
2.15-2.32100.0918.31447114511000.091
2.32-2.559.90.074101331213391000.074
2.55-2.859.90.05812.21209712261000.058
2.85-3.299.70.04614.51049510851000.046
3.29-4.029.50.03815.489499421000.038
4.02-5.6990.03515.467327521000.035
5.69-18.718.50.02819.7366243397.10.028

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→18.71 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.163 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.877 / SU B: 4.69 / SU ML: 0.068 / SU R Cruickshank DPI: 0.113 / SU Rfree: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 578 4.8 %RANDOM
Rwork0.167 ---
obs0.169 12092 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.81 Å2 / Biso mean: 21.23 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---0.5 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms905 0 0 109 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022920
X-RAY DIFFRACTIONr_angle_refined_deg2.1931.9771243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2685114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10125.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3615166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.239156
X-RAY DIFFRACTIONr_chiral_restr0.1550.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021697
X-RAY DIFFRACTIONr_mcbond_it1.2031.5572
X-RAY DIFFRACTIONr_mcangle_it1.9312912
X-RAY DIFFRACTIONr_scbond_it3.9113348
X-RAY DIFFRACTIONr_scangle_it6.034.5331
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 47 -
Rwork0.226 809 -
all-856 -
obs--100 %
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)
117.7145-4.90622.65287.788-9.472212.91880.10440.1189-1.8101-0.5273-0.2628-0.16860.7190.6010.15830.90390.18070.33570.2564-0.08910.742530.23-7.526-3.491
21.5866-1.3333-2.26545.4225.22027.8922-0.0029-0.01580.0808-0.09940.1063-0.22540.14720.1937-0.10330.0970.00110.02380.09650.01780.031924.4338.8123.819
32.31350.367-0.15614.85693.60477.23390.08440.0129-0.0007-0.0313-0.07130.0763-0.1745-0.0237-0.01320.0788-0.0016-0.00060.04990.0040.00314.58920.48215.082
49.9373-2.7034-0.7859.8809-0.8983.7828-0.0974-0.0948-0.2234-0.3348-0.08330.56310.2692-0.31140.18070.15530.0031-0.00310.086-0.03070.047415.5124.0174.418
52.2999-0.8057014.3377016.16220.04760.0183-0.4386-0.9445-0.3163-0.08621.39940.92650.26860.51370.0837-0.0190.1936-0.08060.49422.317-8.424.014
62.7766-2.264-2.48166.9412.07566.0917-0.12070.0514-0.2448-0.2544-0.08370.03230.4809-0.0020.20430.1345-0.02150.01940.07820.00570.028216.6540.49113.949
73.0997-3.0391-1.24375.93542.13163.1137-0.0549-0.13880.03820.12280.04670.01010.02490.08110.00810.0904-0.03290.00140.07410.00910.004215.54712.30920.933
818.7657-9.9326-8.30657.9661.1997.4583-0.1273-0.0401-0.5906-0.4222-0.45930.01430.61160.58560.58660.33720.1733-0.02280.283-0.06640.204827.2160.3538.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 36
2X-RAY DIFFRACTION2A37 - 58
3X-RAY DIFFRACTION3A59 - 80
4X-RAY DIFFRACTION4A81 - 90
5X-RAY DIFFRACTION5A91 - 98
6X-RAY DIFFRACTION6A99 - 112
7X-RAY DIFFRACTION7A113 - 140
8X-RAY DIFFRACTION8A141 - 146

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