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- PDB-7yth: Structure of OCPx1 from Nostoc flagelliforme CCNUN1 -

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Basic information

Entry
Database: PDB / ID: 7yth
TitleStructure of OCPx1 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
Ketosteroid isomerase-related protein
Similarity search - Component
Biological speciesNostoc flagelliforme CCNUN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsYang, Y.W. / Liu, K. / Chen, S.Z. / 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
B: Ketosteroid isomerase-related protein
C: Ketosteroid isomerase-related protein
D: Ketosteroid isomerase-related protein


Theoretical massNumber of molelcules
Total (without water)143,7724
Polymers143,7724
Non-polymers00
Water10,413578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-45 kcal/mol
Surface area54130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.780, 122.950, 141.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ketosteroid isomerase-related protein


Mass: 35943.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc flagelliforme CCNUN1 (bacteria) / Gene: COO91_01637 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K8SJT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.93→79.78 Å / Num. obs: 103819 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.5
Reflection shellResolution: 1.93→1.98 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 7107 / CC1/2: 0.854 / % possible all: 92.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XB5

4xb5


Resolution: 1.93→67.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.536 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 5103 4.9 %RANDOM
Rwork0.1993 ---
obs0.2017 98646 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 128.06 Å2 / Biso mean: 45.511 Å2 / Biso min: 25.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.93→67.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9719 0 0 578 10297
Biso mean---51.39 -
Num. residues----1254
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179295
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.64213513
X-RAY DIFFRACTIONr_angle_other_deg1.3461.56521588
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.81851244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55523.271483
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.379151634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7381551
X-RAY DIFFRACTIONr_chiral_restr0.0770.21340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211080
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022001
LS refinement shellResolution: 1.93→1.978 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.368 358 -
Rwork0.309 6742 -
obs--91.98 %

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