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- PDB-3mg1: Crystal structure of the orange carotenoid protein from cyanobact... -

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Basic information

Entry
Database: PDB / ID: 3mg1
TitleCrystal structure of the orange carotenoid protein from cyanobacteria Synechocystis sp. PCC 6803
ComponentsOrange carotenoid protein
KeywordsCAROTENOID BINDING PROTEIN / Echinone / Phycobilisome
Function / homology
Function and homology information


light absorption / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / 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
beta,beta-caroten-4-one / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.649 Å
AuthorsWilson, A. / Kinney, J. / Zwart, P.H. / Punginelli, C. / D'Haen, S. / Perreau, F. / Klein, M.G. / Kirilovsky, D. / Kerfeld, C.A.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Structural determinants underlying photoprotection in the photoactive orange carotenoid protein of cyanobacteria.
Authors: Wilson, A. / Kinney, J.N. / Zwart, P.H. / Punginelli, C. / D'Haene, S. / Perreau, F. / Klein, M.G. / Kirilovsky, D. / Kerfeld, C.A.
#1: 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.
History
DepositionApr 5, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionApr 14, 2010ID: 3I1V
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,1976
Polymers70,9112
Non-polymers1,2864
Water13,259736
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Orange carotenoid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0983
Polymers35,4551
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Orange carotenoid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0983
Polymers35,4551
Non-polymers6432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.939, 82.939, 87.632
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Detailsdimer

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Components

#1: Protein Orange carotenoid protein / OCP


Mass: 35455.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr1963 / Production host: Escherichia coli (E. coli) / References: UniProt: P74102
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 736 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWATER MOLECULES 1001-1736 IN THE COORDINATES CORRESPOND TO WATER MOLECULES 1-736 IN THE RELEVANT PUBLICATION.

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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: 2.45 Å3/Da / Density % sol: 49.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12% PEG 4000, 100mM Sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2008
RadiationMonochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 80661 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.65-1.713.80.3493.9
1.71-1.784.70.25699.8
1.78-1.866.60.178100
1.86-1.9670.125100
1.96-2.0870.09100
2.08-2.247.10.071100
2.24-2.4670.061100
2.46-2.8270.05100
2.82-3.556.90.053100
3.55-506.70.06299.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXdev_222refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M98

1m98
PDB Unreleased entry


Resolution: 1.649→33.231 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.19 / σ(F): 1.97 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1905 4038 5.01 %
Rwork0.1618 --
obs0.1632 80620 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.72 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso mean: 26.477 Å2
Baniso -1Baniso -2Baniso -3
1--0.9734 Å2-0 Å20 Å2
2---0.9734 Å2-0 Å2
3---1.9469 Å2
Refinement stepCycle: LAST / Resolution: 1.649→33.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4667 0 94 736 5497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065003
X-RAY DIFFRACTIONf_angle_d1.0156843
X-RAY DIFFRACTIONf_dihedral_angle_d17.7781909
X-RAY DIFFRACTIONf_chiral_restr0.064767
X-RAY DIFFRACTIONf_plane_restr0.012910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6493-1.70830.25233610.19857226X-RAY DIFFRACTION94
1.7083-1.77670.19573790.17487756X-RAY DIFFRACTION100
1.7767-1.85750.21034120.17137704X-RAY DIFFRACTION100
1.8575-1.95540.19874020.16157716X-RAY DIFFRACTION100
1.9554-2.07790.19533870.15757789X-RAY DIFFRACTION100
2.0779-2.23830.18244130.15597695X-RAY DIFFRACTION100
2.2383-2.46350.19514250.16467686X-RAY DIFFRACTION100
2.4635-2.81980.21424310.16647663X-RAY DIFFRACTION100
2.8198-3.5520.18024080.15787727X-RAY DIFFRACTION100
3.552-33.2380.16364200.14547620X-RAY DIFFRACTION99
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)
10.54580.12350.12790.14360.22860.9979-0.10930.03770.04380.22390.1086-0.10290.11860.05720.02240.09720.00430.00460.0311-0.02490.1198-21.70259.449427.9843
21.5586-1.0178-0.49481.05080.14620.5561-0.1752-0.0465-0.01930.26540.1162-0.07240.23520.0680.04690.21280.0321-0.03430.0794-0.02650.1396-19.038553.970232.9119
31.0205-0.0827-0.16120.7601-0.14170.9592-0.03880.27810.0412-0.0432-0.0245-0.08750.05990.1990.06590.0972-0.00510.01030.26510.03170.1331-13.805169.46038.6372
40.564-0.38640.31741.837-0.31881.1159-0.02250.19690.11050.0102-0.03230.08390.02810.07510.06250.0787-0.0292-0.01140.16810.04530.1303-23.703773.419411.4018
50.43510.0179-0.10.15830.19061.0798-0.1191-0.0319-0.0473-0.19780.1061-0.1244-0.13280.03650.030.1151-0.0006-0.00460.0488-0.02040.1436-22.031184.331441.4217
61.51991.11210.48941.17240.15650.607-0.17040.04070.0019-0.28110.1063-0.0492-0.23870.07520.04950.2056-0.02950.0340.0725-0.02580.1355-18.894789.662436.4336
71.06140.29010.26490.9395-0.18231.0116-0.0121-0.3065-0.06790.0585-0.0594-0.1098-0.05210.20480.06940.07860.004-0.00840.26350.03580.1226-13.819374.282760.5206
80.49050.2394-0.24041.9482-0.24741.1188-0.0123-0.2086-0.1011-0.0058-0.0420.1016-0.02320.07020.0560.08270.03340.01570.17740.04480.1318-23.903170.254758.0139
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:72)
2X-RAY DIFFRACTION2(chain A and resid 73:169)
3X-RAY DIFFRACTION3(chain A and resid 170:243)
4X-RAY DIFFRACTION4(chain A and resid 244:320)
5X-RAY DIFFRACTION5(chain B and resid 5:72)
6X-RAY DIFFRACTION6(chain B and resid 73:169)
7X-RAY DIFFRACTION7(chain B and resid 170:243)
8X-RAY DIFFRACTION8(chain B and resid 244:320)

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