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- PDB-1vyk: CRYSTAL STRUCTURE OF PSBQ PROTEIN OF PHOTOSYSTEM II FROM HIGHER PLANTS -

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Basic information

Entry
Database: PDB / ID: 1vyk
TitleCRYSTAL STRUCTURE OF PSBQ PROTEIN OF PHOTOSYSTEM II FROM HIGHER PLANTS
ComponentsOXYGEN-EVOLVING ENHANCER PROTEIN 3
KeywordsPHOTOSYSTEM II / OXYGEN-ENHANCER EVOLVING COMPLEX / WATER OXIDIZING COMPLEX / PSBQ / OEE3 / PHOTOSYNTHESIS / CHLOROPLAST / TRANSIT PEPTIDE / THYLAKOID / MEMBRANE
Function / homology
Function and homology information


photosystem II oxygen evolving complex / extrinsic component of membrane / chloroplast thylakoid membrane / photosynthesis / calcium ion binding
Similarity search - Function
Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle / : / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Oxygen-evolving enhancer protein 3, chloroplastic
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsHermoso, J.A. / Balsera, M. / De Las Rivas, J. / Arellano, J.B.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The 1.49 A Resolution Crystal Structure of Psbq from Photosystem II of Spinacia Oleracea Reveals a Ppii Structure in the N-Terminal Region.
Authors: Balsera, M. / Arellano, J.B. / Revuelta, J.L. / De Las Rivas, J. / Hermoso, J.A.
History
DepositionApr 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 13, 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_conn_angle / struct_conn
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_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OXYGEN-EVOLVING ENHANCER PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7354
Polymers16,5451
Non-polymers1903
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)49.938, 49.938, 96.972
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein OXYGEN-EVOLVING ENHANCER PROTEIN 3 / CHLOROPLAST PRECURSOR / OEE3 / 16KDA SUBUNIT OF OXYGEN EVOLVING SYSTEM OF PHOTOSYSTEM II / OEC 16KDA SUBUNIT


Mass: 16544.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12301
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSUBCELLULAR LOCATION: CHLOROPLAST THYLAKOID MEMBRANE; ASSOCIATED WITH THE PHOTOSYSTEM II COMPLEX.

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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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16-18% PEG 6000, 0.1 M MES PH 6.5, 0.3 M ZN ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMP 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 2003 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.49→24.25 Å / Num. obs: 23594 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 9.5
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.2 / % possible all: 99.1

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NZE

1nze


Resolution: 1.49→14.43 Å / SU B: 1.194 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.073
Details: INDIVIDUAL ATOMIC THERMAL FACTORS REFINEMENT AND TLS REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1212 5.2 %RANDOM
Rwork0.163 ---
obs0.164 22309 99.72 %-
Displacement parametersBiso mean: 22.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.49→14.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1025 0 6 264 1295

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