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- PDB-3zsu: Structure of the CyanoQ protein from Thermosynechococcus elongatus -

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Basic information

Entry
Database: PDB / ID: 3zsu
TitleStructure of the CyanoQ protein from Thermosynechococcus elongatus
ComponentsTLL2057 PROTEIN
KeywordsPHOTOSYNTHESIS / PHOTOSYSTEM II ASSEMBLY / EXTRINSIC PROTEIN
Function / homology
Function and homology information


photosystem II oxygen evolving complex / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / photosynthesis / calcium ion binding
Similarity search - Function
Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / 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 speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsMichoux, F. / Takasaka, K. / Nixon, P.J. / Murray, J.W.
CitationJournal: Photosynth.Res. / Year: 2014
Title: Crystal Structure of Cyanoq from the Thermophilic Cyanobacterium Thermosynechococcus Elongatus and Detection in Isolated Photosystem II Complexes.
Authors: Michoux, F. / Boehm, M. / Bialek, W. / Takasaka, K. / Maghlaoui, K. / Barber, J. / Murray, J.W. / Nixon, P.J.
History
DepositionJun 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TLL2057 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4802
Polymers14,3841
Non-polymers961
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.165, 47.165, 106.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

#1: Protein TLL2057 PROTEIN / CYANOQ


Mass: 14384.037 Da / Num. of mol.: 1 / Fragment: MATURE PROTEIN, RESIDUES 23-152 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.39 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growDetails: 1.8 M AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.0722
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 1.6→53.35 Å / Num. obs: 19307 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 6.98 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.85
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.72 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LS0

3ls0


Resolution: 1.6→40.85 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.589 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 963 5.2 %RANDOM
Rwork0.162 ---
obs0.164 17700 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.05 Å20 Å2
2--0.1 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms938 0 5 74 1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022996
X-RAY DIFFRACTIONr_bond_other_d0.0010.02688
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.9821352
X-RAY DIFFRACTIONr_angle_other_deg1.01231674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.785125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98724.71753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64415180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.2511510
X-RAY DIFFRACTIONr_chiral_restr0.120.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2781.5614
X-RAY DIFFRACTIONr_mcbond_other0.4331.5245
X-RAY DIFFRACTIONr_mcangle_it2.5652990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7833382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.3774.5362
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 77 -
Rwork0.222 1300 -
obs--99.93 %
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)
16.11011.19090.53430.2645-0.32235.8693-0.0564-0.4975-0.0451-0.0094-0.1274-0.017-0.12590.34440.18380.04140.0287-0.0140.26160.02920.106430.463215.5057-5.3277
23.32220.21510.78210.7381-0.18430.2744-0.03970.2144-0.0881-0.15310.06610.02850.0480.0747-0.02630.0799-0.0058-0.00570.1591-0.01940.07677.698114.0955-20.8416
30.9370.33650.4490.64660.02251.3173-0.04240.0033-0.1251-0.03260.03560.0260.10340.13430.00680.07290.03350.00670.1282-0.01050.099413.265510.4107-9.149
41.1996-0.19570.90661.08190.04290.74830.0414-0.0804-0.0410.0307-0.00050.1050.0535-0.0327-0.04090.0919-0.0129-0.00690.15890.00950.1384-3.791712.0682-12.3386
51.99650.25830.21941.073-0.0060.35-0.03490.04920.09850.02020.0307-0.02160.01450.03580.00410.1080.0099-0.00080.1612-0.00420.121512.042920.7284-7.9747
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 45
2X-RAY DIFFRACTION2A46 - 73
3X-RAY DIFFRACTION3A74 - 110
4X-RAY DIFFRACTION4A111 - 135
5X-RAY DIFFRACTION5A136 - 151

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