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- PDB-2vu4: Structure of PsbP protein from Spinacia oleracea at 1.98 A resolution -

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Basic information

Entry
Database: PDB / ID: 2vu4
TitleStructure of PsbP protein from Spinacia oleracea at 1.98 A resolution
ComponentsOXYGEN-EVOLVING ENHANCER PROTEIN 2
KeywordsPHOTOSYNTHESIS / 23 KDA PROTEIN / TRANSIT PEPTIDE / HIGHER PLANTS / PHOTOSYSTEM II / MEMBRANE / THYLAKOID / CHLOROPLAST / OXYGEN-EVOLVING COMPLEX
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
PsbP, C-terminal / PsbP / Mog1/PsbP, alpha/beta/alpha sandwich / Mog1/PsbP, alpha/beta/alpha sandwich / Protein Transport Mog1p; Chain A / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxygen-evolving enhancer protein 2, chloroplastic
Similarity search - Component
Biological speciesSPINACIA OLERACEA (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLapkouski, M. / Ristvejova, R. / Arellano, J.B. / Revuelta, J.L. / Kuta Smatanova, I. / Ettrich, R.
CitationJournal: Plos One / Year: 2012
Title: Raman Spectroscopy Adds Complementary Detail to the High-Resolution X-Ray Crystal Structure of Photosynthetic Psbp from Spinacia Oleracea.
Authors: Kopecky, V.J. / Kohoutova, J. / Lapkouski, M. / Hofbauerova, K. / Sovova, Z. / Ettrichova, O. / Gonzalez-Perez, S. / Dulebo, A. / Kaftan, D. / Kuta Smatanova, I. / Revuelta, J.L. / Arellano, ...Authors: Kopecky, V.J. / Kohoutova, J. / Lapkouski, M. / Hofbauerova, K. / Sovova, Z. / Ettrichova, O. / Gonzalez-Perez, S. / Dulebo, A. / Kaftan, D. / Kuta Smatanova, I. / Revuelta, J.L. / Arellano, J.B. / Carey, J. / Ettrich, R.
History
DepositionMay 21, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references / Other ...Database references / Other / Refinement description / Structure summary
Revision 1.3Nov 7, 2012Group: Database references
Revision 1.4Dec 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 / struct_conn / 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_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 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7122
Polymers20,6471
Non-polymers651
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.770, 45.568, 82.495
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 OXYGEN-EVOLVING ENHANCER PROTEIN 2 / OEE2 / 23 KDA SUBUNIT OF OXYGEN EVOLVING SYSTEM OF PHOTOSYSTEM II / 23 KDA THYLAKOID MEMBRANE PROTEIN / PSBP


Mass: 20646.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SPINACIA OLERACEA (spinach) / Plasmid: JR2592 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12302
#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.: 34 / 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: 1.65 Å3/Da / Density % sol: 25.56 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.98→45.55 Å / Num. obs: 9051 / % possible obs: 89.7 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.1
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.8 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V2B

1v2b


Resolution: 1.98→30.59 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.98 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-15,90-107,135-139 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 884 9.9 %RANDOM
Rwork0.181 ---
obs0.186 8009 87.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å20 Å20 Å2
2--1.04 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.98→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1138 0 1 34 1173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221162
X-RAY DIFFRACTIONr_bond_other_d0.0050.02783
X-RAY DIFFRACTIONr_angle_refined_deg2.071.9581571
X-RAY DIFFRACTIONr_angle_other_deg1.26331921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1365145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.98625.41748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.18715194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.023152
X-RAY DIFFRACTIONr_chiral_restr0.2840.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021281
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02227
X-RAY DIFFRACTIONr_nbd_refined0.2170.2150
X-RAY DIFFRACTIONr_nbd_other0.20.2714
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2535
X-RAY DIFFRACTIONr_nbtor_other0.0960.2594
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.219
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_it1.3181.5811
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.78921179
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8943483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0194.5392
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: 1.98→2.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 49
Rwork0.253 525
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)
16.6852.35310.82376.83030.66344.9208-0.26470.3267-0.0089-0.53270.1579-0.3965-0.32180.10240.10680.17560.03840.1238-0.07570.0144-0.012513.4254.5730.301
22.57391.4608-0.81053.8361-0.92811.86720.1615-0.1365-0.07180.1602-0.1094-0.0938-0.04930.0271-0.05210.20790.0430.0376-0.04610.00090.00995.859-1.39111.559
32.343.46222.308216.98219.219211.0560.0060.1820.2518-0.0636-0.03980.0379-0.48880.03760.03390.24250.05270.0424-0.02130.02850.0095.85810.2287.484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 42
2X-RAY DIFFRACTION2A43 - 165
3X-RAY DIFFRACTION3A166 - 186

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