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- PDB-5ui2: CRYSTAL STRUCTURE OF ORANGE CAROTENOID PROTEIN -

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Basic information

Entry
Database: PDB / ID: 5ui2
TitleCRYSTAL STRUCTURE OF ORANGE CAROTENOID PROTEIN
ComponentsOrange carotenoid-binding protein
Keywordscarotenoid binding protein
Function / homology
Function and homology information


light absorption / : / phycobilisome / chloride ion binding / photoreceptor activity
Similarity search - Function
orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / 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 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily ...orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / 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 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
sucrose / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesArthrospira maxima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKERFELD, C.A. / SAWAYA, M.R. / VISHNU, B. / KROGMANN, D. / YEATES, T.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH GM 31299 United States
United States Department of Agriculture (USDA)USDA1999-01759 United States
Citation
Journal: Structure / Year: 2003
Title: The crystal structure of a cyanobacterial water-soluble carotenoid binding protein.
Authors: Kerfeld, C.A. / Sawaya, M.R. / Brahmandam, V. / Cascio, D. / Ho, K.K. / Trevithick-Sutton, C.C. / Krogmann, D.W. / Yeates, T.O.
#1: Journal: ACTA CRYSTALLOGR., SECT.D / Year: 1997
Title: CRYSTALS OF THE CAROTENOID PROTEIN FROM ARTHROSPIRA MAXIMA CONTAINING UNIFORMLY ORIENTED PIGMENT MOLECULES
Authors: KERFELD, C.A. / WU, Y.P. / CHAN, C. / KROGMANN, D.W. / YEATES, T.O.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionJan 25, 2017ID: 1M98
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity.formula_weight
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Structure summary / Category: entity / pdbx_audit_support
Item: _entity.formula_weight / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
B: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2947
Polymers70,7472
Non-polymers1,5475
Water5,765320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-26 kcal/mol
Surface area27580 Å2
Unit cell
Length a, b, c (Å)217.200, 40.761, 75.460
Angle α, β, γ (deg.)90.000, 95.800, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Orange carotenoid-binding protein / OCP


Mass: 35373.363 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arthrospira maxima (bacteria) / References: UniProt: P83689
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EQ3 / (3'R)-3'-hydroxy-beta,beta-caroten-4-one / 3'-Hydroxyechinenone / 3'-OH-Echinenone


Mass: 566.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: PEG 3350, SODIUM CHLORIDE, TRIS, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0094 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 16, 2001 / Details: COLLIMATING MIRROR OPTICS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.1→64.55 Å / Num. obs: 37373 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 29.38 Å2 / Rsym value: 0.065 / Net I/σ(I): 21.7
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.386 / % possible all: 84.3

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.0refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.25 Å / Cor.coef. Fo:Fc: 0.9331 / Cor.coef. Fo:Fc free: 0.8915 / SU R Cruickshank DPI: 0.277 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.285 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1800 4.98 %RANDOM
Rwork0.2129 ---
obs0.2155 36112 92.55 %-
Displacement parametersBiso max: 141.43 Å2 / Biso mean: 41.04 Å2 / Biso min: 13.21 Å2
Baniso -1Baniso -2Baniso -3
1--3.0441 Å20 Å2-0.591 Å2
2---2.0085 Å20 Å2
3---5.0526 Å2
Refine analyzeLuzzati coordinate error obs: 0.418 Å
Refinement stepCycle: final / Resolution: 2.1→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4938 0 109 320 5367
Biso mean--24.14 36.63 -
Num. residues----630
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1846SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes740HARMONIC5
X-RAY DIFFRACTIONt_it5156HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion689SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6297SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5156HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7024HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion2.32
X-RAY DIFFRACTIONt_other_torsion18.24
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3425 130 4.99 %
Rwork0.2806 2477 -
all0.2836 2607 -
obs--92.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13910.32430.04870.90740.2752.5268-0.0192-0.0644-0.0235-0.02870.0293-0.12430.02640.0919-0.010.0108-0.11260.03440.012-0.0205-0.150339.6831-1.98247.0384
20.6578-0.0749-0.05580.575-0.37452.69630.2212-0.14110.04840.12270.01820.0736-0.9350.4199-0.23940.322-0.25820.1569-0.1817-0.0866-0.215314.55723.460127.066
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 317
2X-RAY DIFFRACTION2{ B|* }B2 - 315

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