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- PDB-8pzk: Crystal structure of the Orange Carotenoid Protein 2 (OCP2) from ... -

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Basic information

Entry
Database: PDB / ID: 8pzk
TitleCrystal structure of the Orange Carotenoid Protein 2 (OCP2) from Gloeocapsa sp. PCC 7428
ComponentsOrange carotenoid-binding protein
KeywordsPHOTOSYNTHESIS / photoprotective protein / photosensory protein / OCP2 / carotenoid binding
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding
Similarity search - Function
Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / NTF2-like domain superfamily
Similarity search - Domain/homology
AZIDE ION / beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesGloeocapsa sp. PCC 7428 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBoyko, K.M. / Varfolomeeva, L.A. / Slonimskiy, Y.B. / Maksimov, E.G. / Popov, V.O. / Sluchanko, N.N.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1354 Russian Federation
Russian Science Foundation21-44-00005 Russian Federation
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families.
Authors: Sluchanko, N.N. / Maksimov, E.G. / Slonimskiy, Y.B. / Varfolomeeva, L.A. / Bukhanko, A.Y. / Egorkin, N.A. / Tsoraev, G.V. / Khrenova, M.G. / Ge, B. / Qin, S. / Boyko, K.M. / Popov, V.O.
History
DepositionJul 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3949
Polymers35,4191
Non-polymers9758
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint6 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.661, 52.661, 216.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Orange carotenoid-binding protein


Mass: 35419.230 Da / Num. of mol.: 1 / Mutation: E26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gloeocapsa sp. PCC 7428 (bacteria) / Gene: Glo7428_2455 / Production host: Escherichia coli (E. coli) / References: UniProt: K9XH36

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Non-polymers , 5 types, 104 molecules

#2: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H54O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: N3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 42.04 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium formate dihydrate, 0.1 M Sodium acetate trihydrate pH 4.0, 18% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→72.28 Å / Num. obs: 29081 / % possible obs: 98.2 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.072 / Rrim(I) all: 0.153 / Χ2: 1.01 / Net I/σ(I): 6.6 / Num. measured all: 125097
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 92.3 % / Redundancy: 4.4 % / Rmerge(I) obs: 2.668 / Num. measured all: 6915 / Num. unique obs: 1584 / CC1/2: 0.283 / Rpim(I) all: 1.414 / Rrim(I) all: 3.031 / Χ2: 0.95 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→54.208 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.179 / SU B: 10.682 / SU ML: 0.146 / Average fsc free: 0.9351 / Average fsc work: 0.9501 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.139
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 1498 5.182 %RANDOM
Rwork0.1974 27411 --
all0.2 ---
obs-28909 98.043 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.141 Å2
Baniso -1Baniso -2Baniso -3
1-0.668 Å2-0 Å2-0 Å2
2--0.668 Å2-0 Å2
3----1.337 Å2
Refinement stepCycle: LAST / Resolution: 1.8→54.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 70 96 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122499
X-RAY DIFFRACTIONr_bond_other_d0.0030.0162374
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.653401
X-RAY DIFFRACTIONr_angle_other_deg0.6741.5645459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.96527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.210400
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.28210110
X-RAY DIFFRACTIONr_chiral_restr0.090.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022924
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02564
X-RAY DIFFRACTIONr_nbd_refined0.2110.2512
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1610.22153
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21215
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21386
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2101
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.225
X-RAY DIFFRACTIONr_nbd_other0.1170.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1120.210
X-RAY DIFFRACTIONr_mcbond_it2.352.1921209
X-RAY DIFFRACTIONr_mcbond_other2.3472.1911208
X-RAY DIFFRACTIONr_mcangle_it3.4423.9161502
X-RAY DIFFRACTIONr_mcangle_other3.4453.921503
X-RAY DIFFRACTIONr_scbond_it3.5992.5641290
X-RAY DIFFRACTIONr_scbond_other3.5612.5641289
X-RAY DIFFRACTIONr_scangle_it5.2334.5391893
X-RAY DIFFRACTIONr_scangle_other5.224.5411893
X-RAY DIFFRACTIONr_lrange_it6.97924.1712786
X-RAY DIFFRACTIONr_lrange_other6.98624.182787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.8-1.8470.371220.3819530.3821180.8610.86697.96980.359
1.847-1.8970.3251160.34519280.34320870.8890.88697.93960.322
1.897-1.9520.409980.33318920.33620250.8640.89698.27160.303
1.952-2.0120.342960.28418290.28619590.910.9398.26440.246
2.012-2.0780.2621050.25917540.25918860.9480.94798.56840.22
2.078-2.1510.277950.23817120.2418370.9430.95798.36690.205
2.151-2.2320.277790.21216930.21518030.9460.96598.28060.178
2.232-2.3230.272890.21416030.21717330.9470.96697.63420.176
2.323-2.4260.227730.20315480.20416410.9580.97198.78120.169
2.426-2.5440.261890.19114880.19515970.9560.97498.74770.161
2.544-2.6810.306860.20114430.20715360.9470.97399.54430.172
2.681-2.8440.273690.18113410.18614170.9560.97899.5060.158
2.844-3.0390.253720.17112860.17513670.9610.9899.34160.154
3.039-3.2820.237630.17412280.17712990.9650.97999.38410.159
3.282-3.5940.222670.18210980.18411770.9710.98198.98050.177
3.594-4.0160.248510.18610070.1910870.9690.9897.33210.188
4.016-4.6330.183420.1368890.1389720.9780.98995.78190.143
4.633-5.6640.19410.1577690.1588340.9840.98897.12230.161
5.664-7.9670.171240.1596100.1596820.9840.98592.96190.168
7.967-54.2080.182210.1813390.1824280.9830.97584.11220.205
Refinement TLS params.Method: refined / Origin x: 1.4748 Å / Origin y: -23.156 Å / Origin z: 0.6181 Å
111213212223313233
T0.1202 Å2-0.0257 Å20.005 Å2-0.1112 Å2-0.0074 Å2--0.0021 Å2
L0.6191 °2-0.3042 °20.5564 °2-0.5354 °2-0.3904 °2--1.6352 °2
S0.0112 Å °0.0061 Å °-0.0264 Å °-0.0138 Å °0.004 Å °0.0014 Å °0.0418 Å °0.0534 Å °-0.0152 Å °
Refinement TLS groupSelection: ALL

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