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- PDB-6yx8: The structure of allophycocyanin from cyanobacterium Nostoc sp. W... -

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Basic information

Entry
Database: PDB / ID: 6yx8
TitleThe structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.
Components
  • ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
  • BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
KeywordsPHOTOSYNTHESIS / Allophycocyanin crystal structure Phycobilisome Phycobiliproteins Phycocyanobilin chromophore Light harvesting complex Cyanobacterium Nostoc sp. WR13
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Chem-PXQ / Allophycocyanin alpha / Allophycocyanin beta
Similarity search - Component
Biological speciesNostoc sp. WR13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.831 Å
AuthorsPatel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J.
Funding support United States, India, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 (Office of Basic Energy Sciences) United States
Department of Biotechnology (DBT, India)BT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship) India
Department of Biotechnology (DBT, India)BT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship) India
CitationJournal: To Be Published
Title: The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13
Authors: Patel, H.M. / Roszak, A.W. / Madamwar, D. / Cogdell, R.J.
History
DepositionApr 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
BBB: BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
CCC: ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
DDD: BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
EEE: ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
FFF: BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,816105
Polymers103,0446
Non-polymers13,77299
Water16,718928
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36470 Å2
ΔGint-9 kcal/mol
Surface area41120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.676, 177.340, 122.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11BBB-481-

HOH

21EEE-366-

HOH

31EEE-435-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA CCC
22Chains AAA EEE
33Chains BBB DDD
44Chains BBB FFF
55Chains CCC EEE
66Chains DDD FFF

NCS ensembles :
IDDetails
5Chains CCC EEE
1Chains AAA CCC
2Chains AAA EEE
3Chains BBB DDD
4Chains BBB FFF
6Chains DDD FFF

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Components

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Protein , 2 types, 6 molecules AAACCCEEEBBBDDDFFF

#1: Protein ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN


Mass: 17007.270 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN ALPHA SUBUNIT RESIDUE CYS80; The N-terminal Methionine present in the gene sequence ...Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN ALPHA SUBUNIT RESIDUE CYS80; The N-terminal Methionine present in the gene sequence was post-translationally removed and is not present in the crystal structure
Source: (natural) Nostoc sp. WR13 (bacteria)
Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India
References: UniProt: A0A4Y5PW22
#2: Protein BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN


Mass: 17340.707 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Details: THERE IS ONE CHROMOPHORE MOLECULE, PHYCOCYANOBILIN (LIGAND ID: CYC), BOUND COVALENTLY TO ALLOPHYCOCYANIN BETA SUBUNIT RESIDUE CYS81
Source: (natural) Nostoc sp. WR13 (bacteria)
Plasmid details: From the desert Rann of Kachchh (RoK), Gujarat, India
References: UniProt: A0A4Y5PW23

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Non-polymers , 10 types, 1027 molecules

#3: Chemical
ChemComp-PXQ / 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid


Mass: 590.710 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C33H42N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.7 % / Description: Blue color plates with orthorhombic morphology
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus screen condition E12: 37.5% v/v Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; 0.1M Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 0.12M Additives: 0.3M ethylene glycols

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.831→90.144 Å / Num. obs: 87249 / % possible obs: 95.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.15 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.053 / Rrim(I) all: 0.137 / Net I/σ(I): 9.3
Reflection shellResolution: 1.831→1.941 Å / Rmerge(I) obs: 1.278 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4360 / CC1/2: 0.599 / Rpim(I) all: 0.524 / Rrim(I) all: 1.278 / % possible all: 58.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJan 26, 2018 (20180409)data reduction
Aimless0.7.1data scaling
autoPROC1.0.5data scaling
STARANISO1.10.15data scaling
PHASER2.8.3phasing
Coot0.8.9.2 EL (ccp4)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YX7

6yx7


Resolution: 1.831→90.144 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 7.48 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1983 4339 4.973 %
Rwork0.1595 --
all0.161 --
obs-87257 87.265 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.791 Å2
Baniso -1Baniso -2Baniso -3
1-0.262 Å20 Å20 Å2
2---0.452 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.831→90.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7224 0 936 928 9088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0138556
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178533
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.67611417
X-RAY DIFFRACTIONr_angle_other_deg1.3511.59819695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1851051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27420.278431
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.545151330
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg13.127156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5671568
X-RAY DIFFRACTIONr_chiral_restr0.0830.21064
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029288
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021675
X-RAY DIFFRACTIONr_nbd_refined0.2130.21979
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.27379
X-RAY DIFFRACTIONr_nbtor_refined0.1620.23951
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.23266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2778
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1350.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2390.261
X-RAY DIFFRACTIONr_nbd_other0.2550.2193
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2550.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2240.21
X-RAY DIFFRACTIONr_mcbond_it1.7492.8193948
X-RAY DIFFRACTIONr_mcbond_other1.7452.8183947
X-RAY DIFFRACTIONr_mcangle_it2.5564.2154950
X-RAY DIFFRACTIONr_mcangle_other2.5584.2164951
X-RAY DIFFRACTIONr_scbond_it2.5213.2414608
X-RAY DIFFRACTIONr_scbond_other2.5213.2414609
X-RAY DIFFRACTIONr_scangle_it4.0054.6746416
X-RAY DIFFRACTIONr_scangle_other4.0054.6746417
X-RAY DIFFRACTIONr_lrange_it6.71136.2819835
X-RAY DIFFRACTIONr_lrange_other6.33835.369569
X-RAY DIFFRACTIONr_ncsr_local_group_10.0990.054950
X-RAY DIFFRACTIONr_ncsr_local_group_20.0950.054927
X-RAY DIFFRACTIONr_ncsr_local_group_30.0920.054971
X-RAY DIFFRACTIONr_ncsr_local_group_40.0960.054974
X-RAY DIFFRACTIONr_ncsr_local_group_50.1020.054933
X-RAY DIFFRACTIONr_ncsr_local_group_60.1110.054927
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.831-1.8790.256420.2616760.2673380.8470.8339.78470.258
1.879-1.930.2531250.26725270.26670990.840.82737.35740.266
1.93-1.9860.2812510.25653970.25769790.8230.82980.92850.253
1.986-2.0470.2443070.22661950.22767290.8860.88896.62650.218
2.047-2.1140.2313340.20561660.20665460.9070.91499.29730.191
2.114-2.1890.2152610.19261100.19363740.9270.92999.95290.175
2.189-2.2710.2293420.18257580.18561010.9250.93699.98360.164
2.271-2.3640.2153280.16555400.16858710.9310.94799.94890.147
2.364-2.4690.1972860.14753870.1556770.9480.95899.92950.131
2.469-2.5890.1952310.14951810.15154140.9480.95799.96310.134
2.589-2.7290.1972680.13148970.13451650.9530.9671000.12
2.729-2.8950.1782770.12746070.12948840.9620.9711000.119
2.895-3.0940.1922960.13843120.14246110.9520.96599.93490.134
3.094-3.3420.191990.14241050.14543040.9550.9641000.143
3.342-3.660.1722230.12737340.12939580.9650.97399.97470.132
3.66-4.0920.1721440.12434550.12636000.9650.97499.97220.137
4.092-4.7230.1481380.12130580.12232000.9730.97799.8750.142
4.723-5.780.221130.17326050.17527210.9560.95999.88970.203
5.78-8.1580.241180.23220170.23221370.9340.93399.90640.266
8.158-90.1440.205560.23411910.23312520.960.94799.60060.319
Refinement TLS params.Method: refined / Origin x: 12.4712 Å / Origin y: 47.9319 Å / Origin z: 23.9665 Å
111213212223313233
T0.0057 Å20.0095 Å2-0.0036 Å2-0.0538 Å20.0045 Å2--0.0121 Å2
L0.0321 °2-0.0441 °20.0296 °2-0.1481 °2-0.02 °2--0.0326 °2
S0.0018 Å °-0.0079 Å °-0.01 Å °-0.0146 Å °0.0087 Å °0.0076 Å °-0.0002 Å °-0.0022 Å °-0.0104 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 999
2X-RAY DIFFRACTION1ALLBBB1 - 999
3X-RAY DIFFRACTION1ALLCCC1 - 999
4X-RAY DIFFRACTION1ALLDDD1 - 999
5X-RAY DIFFRACTION1ALLEEE1 - 999
6X-RAY DIFFRACTION1ALLFFF1 - 999
7X-RAY DIFFRACTION1ALLWWW1 - 999

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