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- PDB-5g3a: PsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10 -

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Basic information

Entry
Database: PDB / ID: 5g3a
TitlePsbO subunit of Photosystem II, beta barrel domain at 100K, pH 10
ComponentsPHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE
KeywordsPHOTOSYNTHESIS / CARBOXYLATE CLUSTER / PH / PROTON ANTENNA
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / plasma membrane-derived thylakoid membrane
Similarity search - Function
Photosystem II, cytochrome c-550 precursor / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Photosystem II extrinsic protein O
Similarity search - Component
Biological speciesTHERMOSYNECHOCOCCUS ELONGATUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.224 Å
AuthorsBommer, M. / Bondar, A.N. / Zouni, A. / Dobbek, H. / Dau, H.
CitationJournal: Biochemistry / Year: 2016
Title: Crystallographic and Computational Analysis of the Barrel Part of the Psbo Protein of Photosystem II -Carboxylate-Water Clusters as Putative Proton Transfer Relays and Structural Switches
Authors: Bommer, M. / Bondar, A.N. / Zouni, A. / Dobbek, H. / Dau, H.
History
DepositionApr 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Mar 6, 2019Group: Data collection / Database references / Experimental preparation
Category: exptl_crystal_grow / struct_ref_seq
Item: _exptl_crystal_grow.method / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Jan 10, 2024Group: 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_conn_angle / struct_conn / struct_sheet / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6622
Polymers18,6221
Non-polymers401
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.695, 54.695, 192.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

21A-2158-

HOH

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Components

#1: Protein PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE / MSP / PSBO SUBUNIT OF PHOTOSYSTEM II


Mass: 18621.721 Da / Num. of mol.: 1 / Fragment: BETA BARREL DOMAIN, RESIDUES 45-272
Source method: isolated from a genetically manipulated source
Details: LOOPS 55-63,149-192 AND 220-231 DELETED
Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria)
Strain: BP-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A432
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLOOPS 55-63, 149-192 AND 220-231 REPLACED WITH A BETA HAIRPIN OF SEQUENCE NG

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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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE
Crystal growMethod: vapor diffusion / pH: 10
Details: VAPOR DIFFUSION 30 MG/ML PROTEIN, 0.1 M MES-NA PH 6, 0.2 M CALCIUM ACETATE, 30% PEG 400, 0.01 M TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2015 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.22→45.99 Å / Num. obs: 51297 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 18.8 % / Biso Wilson estimate: 12.99 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.57
Reflection shellResolution: 1.22→1.27 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 1.73 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3WU2

3wu2


Resolution: 1.224→45.994 Å / SU ML: 0.11 / σ(F): 1.36 / Phase error: 17.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1793 2100 4.1 %
Rwork0.1535 --
obs0.1546 51284 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.224→45.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 1 162 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121415
X-RAY DIFFRACTIONf_angle_d1.1681928
X-RAY DIFFRACTIONf_dihedral_angle_d22.386529
X-RAY DIFFRACTIONf_chiral_restr0.099227
X-RAY DIFFRACTIONf_plane_restr0.007259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2241-1.25260.27441350.23243169X-RAY DIFFRACTION98
1.2526-1.28390.25941360.2143191X-RAY DIFFRACTION100
1.2839-1.31860.22921370.18923207X-RAY DIFFRACTION100
1.3186-1.35740.23471370.18063222X-RAY DIFFRACTION100
1.3574-1.40120.221390.16023234X-RAY DIFFRACTION100
1.4012-1.45130.2261370.14723210X-RAY DIFFRACTION100
1.4513-1.50940.19121380.13143233X-RAY DIFFRACTION100
1.5094-1.57810.17251390.12363255X-RAY DIFFRACTION100
1.5781-1.66140.13851390.1193261X-RAY DIFFRACTION100
1.6614-1.76540.16471400.12333275X-RAY DIFFRACTION100
1.7654-1.90180.15451390.12293263X-RAY DIFFRACTION100
1.9018-2.09310.15351410.12223296X-RAY DIFFRACTION100
2.0931-2.3960.16271420.13373332X-RAY DIFFRACTION100
2.396-3.01860.17731450.16453407X-RAY DIFFRACTION100
3.0186-46.02650.1841560.17673629X-RAY DIFFRACTION100

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