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- PDB-4k7b: Crystal structure of Extrinsic protein in photosystem II -

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Basic information

Entry
Database: PDB / ID: 4k7b
TitleCrystal structure of Extrinsic protein in photosystem II
ComponentsExtrinsic protein in photosystem II
KeywordsPHOTOSYNTHESIS
Function / homologySodium ion translocating NADH-quinone reductase subunit C-like / Photosystem II Psb31 protein / Photosystem II Psb31 protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Extrinsic protein in photosystem II
Function and homology information
Biological speciesChaetoceros gracilis (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS, MOLECULAR REPLACEMENT / SIRAS / molecular replacement / Resolution: 1.55 Å
AuthorsNagao, R. / Suga, M. / Niikura, A. / Okumura, A. / Koua, F.H.M. / Suzuki, T. / Tomo, T. / Enami, I. / Shen, J.R.
CitationJournal: Biochemistry / Year: 2013
Title: Crystal Structure of Psb31, a Novel Extrinsic Protein of Photosystem II from a Marine Centric Diatom and Implications for Its Binding and Function
Authors: Nagao, R. / Suga, M. / Niikura, A. / Okumura, A. / Koua, F.H. / Suzuki, T. / Tomo, T. / Enami, I. / Shen, J.R.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Extrinsic protein in photosystem II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5584
Polymers13,2741
Non-polymers2843
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.411, 92.411, 31.283
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

21A-380-

HOH

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Components

#1: Protein Extrinsic protein in photosystem II


Mass: 13273.858 Da / Num. of mol.: 1 / Fragment: UNP residues 56-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetoceros gracilis (Diatom) / Gene: psb31 / Production host: Escherichia coli (E. coli) / References: UniProt: B6ZHE7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.9 Å3/Da / Density % sol: 57.66 % / Mosaicity: 0.17 °
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.547→50 Å / Num. obs: 22604 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.05 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.387 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.585.10.49911261.022199.5
1.58-1.615.70.43711081.0981100
1.61-1.645.90.43111321.0961100
1.64-1.676.10.38111151.0711100
1.67-1.716.20.32311071.0551100
1.71-1.756.20.28711581.1131100
1.75-1.796.30.25410831.1421100
1.79-1.846.20.18911461.1671100
1.84-1.896.30.18311031.1631100
1.89-1.956.20.14911361.2041100
1.95-2.026.30.11911211.2171100
2.02-2.16.20.10111331.2911100
2.1-2.26.30.08711241.4221100
2.2-2.326.30.08711301.7721100
2.32-2.466.10.08411322.151199.9
2.46-2.6560.07511402.256199.8
2.65-2.925.90.06511322.335199.7
2.92-3.346.10.05411412.185199.7
3.34-4.216.20.02911501.148199.2
4.21-5060.02311870.801197.8

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Phasing

Phasing
Method
SIRAS
molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
SHELXphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SIRAS, MOLECULAR REPLACEMENT / Resolution: 1.55→30.249 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.13 / σ(F): 1.94 / Phase error: 19.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1949 1118 4.99 %
Rwork0.1855 21308 -
obs0.186 22426 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.52 Å2 / Biso mean: 21.3791 Å2 / Biso min: 8.48 Å2
Refinement stepCycle: LAST / Resolution: 1.55→30.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 16 99 942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007906
X-RAY DIFFRACTIONf_angle_d1.1661230
X-RAY DIFFRACTIONf_chiral_restr0.077131
X-RAY DIFFRACTIONf_plane_restr0.005163
X-RAY DIFFRACTIONf_dihedral_angle_d11.744345
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.62050.22071240.220826222746100
1.6205-1.7060.2261400.204626242764100
1.706-1.81280.23971510.191726532804100
1.8128-1.95280.20221430.176926802823100
1.9528-2.14930.18631570.180925972754100
2.1493-2.46010.21991440.176326652809100
2.4601-3.0990.19351290.189627112840100
3.099-30.25430.17091300.18272756288699
Refinement TLS params.Method: refined / Origin x: 42.9653 Å / Origin y: -13.5112 Å / Origin z: -13.9442 Å
111213212223313233
T0.1467 Å20.0243 Å2-0.0131 Å2-0.0697 Å20.0101 Å2--0.0909 Å2
L1.1185 °20.5905 °2-0.2969 °2-0.7536 °2-0.0043 °2--1.024 °2
S0.0715 Å °0.0414 Å °0.0147 Å °0.0547 Å °-0.039 Å °0 Å °-0.0988 Å °-0.0939 Å °-0.0252 Å °
Refinement TLS groupSelection details: ALL

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