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- PDB-4ri3: Crystal structure of DCCD-modified PsbS from spinach -

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Basic information

Entry
Database: PDB / ID: 4ri3
TitleCrystal structure of DCCD-modified PsbS from spinach
ComponentsPhotosystem II 22 kDa protein, chloroplastic
KeywordsMEMBRANE PROTEIN / transmembrane helices / photo protection / DCCD-modified
Function / homology
Function and homology information


photosystem II / chloroplast thylakoid membrane / photosynthesis / phosphoprotein binding / identical protein binding
Similarity search - Function
Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
DICYCLOHEXYLUREA / : / Photosystem II 22 kDa protein, chloroplastic
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å
AuthorsFan, M. / Li, M. / Chang, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structures of the PsbS protein essential for photoprotection in plants.
Authors: Fan, M. / Li, M. / Liu, Z. / Cao, P. / Pan, X. / Zhang, H. / Zhao, X. / Zhang, J. / Chang, W.
History
DepositionOct 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem II 22 kDa protein, chloroplastic
B: Photosystem II 22 kDa protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,17515
Polymers45,0962
Non-polymers3,07813
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-170 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.704, 77.697, 93.159
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 Photosystem II 22 kDa protein, chloroplastic / CP22


Mass: 22548.221 Da / Num. of mol.: 2 / Fragment: UNP residues 63-274 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q02060
#2: Chemical ChemComp-DCW / DICYCLOHEXYLUREA


Mass: 224.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H24N2O
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 100 mM sodium acetate, 25% PEG 300, 1% ethyl acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2012
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 14787 / Num. obs: 14771 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.7→39.061 Å / SU ML: 0.32 / σ(F): 1.33 / Phase error: 29.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2842 1467 9.93 %
Rwork0.2322 --
obs0.2372 14771 99.44 %
all-14787 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 123 3 2642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052681
X-RAY DIFFRACTIONf_angle_d0.7633603
X-RAY DIFFRACTIONf_dihedral_angle_d14.24960
X-RAY DIFFRACTIONf_chiral_restr0.047431
X-RAY DIFFRACTIONf_plane_restr0.003442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.79530.30881460.26911276X-RAY DIFFRACTION98
2.7953-2.90720.33551390.24171312X-RAY DIFFRACTION100
2.9072-3.03940.28431450.24141307X-RAY DIFFRACTION100
3.0394-3.19960.33031470.2461326X-RAY DIFFRACTION100
3.1996-3.40.29731480.2311315X-RAY DIFFRACTION100
3.4-3.66230.26151430.21921322X-RAY DIFFRACTION100
3.6623-4.03050.26721440.2171338X-RAY DIFFRACTION100
4.0305-4.61290.25241480.20961335X-RAY DIFFRACTION100
4.6129-5.80870.3041530.23511363X-RAY DIFFRACTION100
5.8087-39.06540.281540.24761410X-RAY DIFFRACTION98

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