[English] 日本語
Yorodumi
- PDB-3mg3: Crystal structure of the orange carotenoid protein R155L mutant f... -

+
Open data


ID or keywords:

Loading...

-
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 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: 1.702 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more