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- PDB-3mg3: Crystal structure of the orange carotenoid protein R155L mutant f... -

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Basic information

Entry
Database: PDB / ID: 3mg3
TitleCrystal structure of the orange carotenoid protein R155L mutant from cyanobacteria synechocystis sp. PCC 6803
ComponentsOrange carotenoid-binding 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 (NTF2) domain / Nuclear transport factor 2 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 (NTF2) domain / Nuclear transport factor 2 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: 1.702 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: 3I1X
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 6, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)72,56911
Polymers70,8232
Non-polymers1,7469
Water11,674648
1


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


Theoretical massNumber of molelcules
Total (without water)36,2395
Polymers35,4111
Non-polymers8274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3316
Polymers35,4111
Non-polymers9195
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.683, 82.683, 86.571
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-binding protein / OCP


Mass: 35411.375 Da / Num. of mol.: 2 / Mutation: R155L
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-ECH / beta,beta-caroten-4-one / echinenone


Mass: 550.856 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H54O
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsWATER MOLECULES 1001-1648 IN THE COORDINATES CORRESPOND TO WATER MOLECULES 1-648 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 12% PEG 3350, 100mM Sodium acetate, 2% Glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2009
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: 1.7→50 Å / Num. obs: 71874 / % possible obs: 99 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.7-1.735.70.55198
1.73-1.765.70.4898.1
1.76-1.795.70.41198.3
1.79-1.835.80.32998.4
1.83-1.875.70.27398.4
1.87-1.915.70.22398.6
1.91-1.965.70.18698.7
1.96-2.025.80.15198.8
2.02-2.075.70.13399.1
2.07-2.145.70.11599.2
2.14-2.225.80.10398.8
2.22-2.315.70.09799.5
2.31-2.415.70.08599.2
2.41-2.545.70.08199.5
2.54-2.75.70.07599.6
2.7-2.915.70.0799.6
2.91-3.25.70.06899.8
3.2-3.665.60.05799.8
3.66-4.615.50.04799.8
4.61-505.90.04499.8

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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 3I1V

3i1v
PDB Unreleased entry


Resolution: 1.702→41.341 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.17 / σ(F): 1.97 / Phase error: 18.91 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.1907 3614 5.03 %
Rwork0.1533 --
obs0.1552 71837 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.924 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso mean: 23.164 Å2
Baniso -1Baniso -2Baniso -3
1--0.6686 Å2-0 Å20 Å2
2---0.6686 Å2-0 Å2
3---1.3372 Å2
Refinement stepCycle: LAST / Resolution: 1.702→41.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4653 0 124 648 5425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145048
X-RAY DIFFRACTIONf_angle_d1.4326904
X-RAY DIFFRACTIONf_dihedral_angle_d18.0231924
X-RAY DIFFRACTIONf_chiral_restr0.093780
X-RAY DIFFRACTIONf_plane_restr0.014910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7025-1.76330.24693340.20026810X-RAY DIFFRACTION98
1.7633-1.83390.22973490.17846766X-RAY DIFFRACTION98
1.8339-1.91740.2063550.15616772X-RAY DIFFRACTION99
1.9174-2.01850.18133440.14996859X-RAY DIFFRACTION99
2.0185-2.14490.19713610.14566822X-RAY DIFFRACTION99
2.1449-2.31050.18333620.13866812X-RAY DIFFRACTION99
2.3105-2.5430.19543950.14686807X-RAY DIFFRACTION99
2.543-2.91090.1973730.15036839X-RAY DIFFRACTION100
2.9109-3.66710.17543720.14426863X-RAY DIFFRACTION100
3.6671-41.35370.17933690.15576873X-RAY DIFFRACTION100
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)
10.3527-0.00330.20470.04390.19561.0019-0.11070.02760.07170.12160.04450.01370.12820.04810.07360.07190.01180.00760.0229-0.0270.0567-21.443311.2423-2.3099
21.6758-0.7659-0.49940.35450.16150.6027-0.1858-0.0236-0.03730.15140.0990.020.21080.04380.07330.12260.039-0.01050.0316-0.01690.0423-18.90096.00322.8715
30.3503-0.231-0.19830.5581-0.21360.6945-0.03690.1470.0546-0.0491-0.0991-0.12760.03040.31170.11450.02040.00630.0130.19510.05140.051-13.546721.2433-21.1868
40.0942-0.12610.22010.328-0.09350.7206-0.03660.12260.02640.0206-0.06110.00310.03610.12030.07740.0048-0.0316-0.02050.06730.04330.0353-23.942425.5305-18.6306
50.20580.0217-0.1330.04110.17930.966-0.1077-0.0106-0.0778-0.10220.0585-0.0031-0.10770.04680.05840.0735-0.0104-0.00050.0311-0.02540.0722-21.848736.339111.4104
61.67350.66320.42810.30480.01180.6541-0.17970.02430.0202-0.12490.09860.0024-0.22570.03120.07270.1239-0.04250.01320.0302-0.02310.0469-18.957341.5916.2795
70.32020.20880.14240.3575-0.17930.5856-0.0314-0.1483-0.070.0296-0.0817-0.0904-0.02620.25860.09760.0148-0.0027-0.00970.16860.0440.0382-13.606426.352830.3996
80.14260.1888-0.29090.6586-0.17850.6713-0.0172-0.1125-0.0107-0.0118-0.0560.0491-0.02190.12370.06260.02040.03120.01030.06370.03680.0396-23.477722.210427.8956
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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