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- PDB-7ytf: Structure of OCPx2 from Nostoc flagelliforme CCNUN1 -

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Basic information

Entry
Database: PDB / ID: 7ytf
TitleStructure of OCPx2 from Nostoc flagelliforme CCNUN1
ComponentsKetosteroid isomerase-related protein
KeywordsPHOTOSYNTHESIS / OCP protein
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / isomerase activity
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
beta,beta-carotene-4,4'-dione / Ketosteroid isomerase-related protein
Similarity search - Component
Biological speciesNostoc flagelliforme CCNUN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsYang, Y.W. / Chen, S.Z. / Liu, K. / Chen, M. / Qiu, B.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670332 China
CitationJournal: Plant Physiol. / Year: 2023
Title: Functional specialization of expanded orange carotenoid protein paralogs in subaerial Nostoc species.
Authors: Yang, Y.W. / Liu, K. / Huang, D. / Yu, C. / Chen, S.Z. / Chen, M. / Qiu, B.S.
History
DepositionAug 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ketosteroid isomerase-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7672
Polymers36,2021
Non-polymers5651
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.635, 154.635, 86.866
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Ketosteroid isomerase-related protein


Mass: 36202.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc flagelliforme CCNUN1 (bacteria) / Gene: COO91_05528 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K8SVQ4
#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS pH 5.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.65→66.96 Å / Num. obs: 18058 / % possible obs: 98.6 % / Redundancy: 39.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 29.5
Reflection shellResolution: 2.65→2.78 Å / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2372 / CC1/2: 0.985 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB5

4xb5


Resolution: 2.65→44.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.617 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2565 941 5.2 %RANDOM
Rwork0.1988 ---
obs0.2017 17098 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 187.16 Å2 / Biso mean: 66.57 Å2 / Biso min: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 2.65→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2405 0 42 52 2499
Biso mean--65.36 64.45 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172310
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6493407
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5675352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.615307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69521.972142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9521510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02514
LS refinement shellResolution: 2.65→2.719 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 74 -
Rwork0.279 1243 -
all-1317 -
obs--99.92 %

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