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- PDB-1nze: Crystal structure of PsbQ polypeptide of photosystem II from high... -

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Basic information

Entry
Database: PDB / ID: 1nze
TitleCrystal structure of PsbQ polypeptide of photosystem II from higher plants
ComponentsOxygen-evolving enhancer protein 3
KeywordsOXIDOREDUCTASE / Photosystem II / oxygen-enhancer evolving complex / water oxidizing complex / PsbQ / OEE3
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosynthetic electron transport chain / extrinsic component of membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / chloroplast thylakoid membrane / 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
Oxygen-evolving enhancer protein 3, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsCalderone, V. / Trabucco, M. / Vujicic, A. / Battistutta, R. / Giacometti, G.M. / Andreucci, F. / Barbato, R. / Zanotti, G.
Citation
Journal: Embo Rep. / Year: 2003
Title: Crystal structure of the PsbQ protein of photosystem II from higher plants
Authors: Calderone, V. / Trabucco, M. / Vujicic, A. / Battistutta, R. / Giacometti, G.M. / Andreucci, F. / Barbato, R. / Zanotti, G.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Excited State Dynamics in Photosystem II: Insights from the X-Ray Crystal Structure
Authors: Vasilev, S. / Orth, P. / Zouni, A. / Owens, T.G. / Bruce, D.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Three-dimensional electron cryo-microscopy study of the extrinsic domains of the oxygen-evolving complex of spinach: assignment of the PsbO protein
Authors: Nield, J. / Balsera, M. / De Las Rivas, J. / Barber, J.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of oxygen-evolving photosystem II from Thermosynechoccus vulcanus at 3.7 A resolution
Authors: Kamiyam, N. / Shen, J.-R.
History
DepositionFeb 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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: Oxygen-evolving enhancer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6102
Polymers16,5451
Non-polymers651
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.282, 50.282, 94.067
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 / OEE3 / 16 kDa subunit of oxygen evolving system of photosystem II / OEC 16 kDa subunit / PsbQ


Mass: 16544.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The protein was extracted from PS II thylacoid membranes
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12301
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM Tris, 50 mM NaCl, 5 mM Zn2+, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120-24 mg/mlprotein1drop
225-30 %(w/v)PEG33501reservoiror PDB4000
35 mM1reservoirpH4.6Zn2+

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2910.93, 1.282, 1.284
SYNCHROTRONELETTRA 5.2R21.2
SYNCHROTRONESRF ID14-430.9393
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDFeb 15, 2002
MARRESEARCH2CCDSep 4, 2001
ADSC QUANTUM 43CCDApr 9, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.931
21.2821
31.2841
41.21
50.93931
ReflectionResolution: 1.95→43.55 Å / Num. all: 10333 / Num. obs: 10333 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 3.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1340 / Rsym value: 0.33 / % possible all: 90.9
Reflection
*PLUS
Lowest resolution: 39 Å / Redundancy: 8.9 %
Reflection shell
*PLUS
% possible obs: 90.9 % / Num. unique obs: 1340

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.95→43.55 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1062 10.3 %RANDOM
Rwork0.227 ---
all0.229 10333 --
obs0.227 10307 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 77.2503 Å2 / ksol: 0.368844 e/Å3
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.56 Å22.22 Å20 Å2
2---6.75 Å20 Å2
3---11.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 1.95→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms876 0 1 73 950
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.842
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_scangle_it4.032.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 158 10.3 %
Rwork0.382 1379 -
obs-1560 90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97

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