[English] 日本語
Yorodumi
- PDB-6yx7: The high resolution structure of allophycocyanin from cyanobacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yx7
TitleThe high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.
Components(Allophycocyanin ...) x 2
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
ALANINE / PHYCOCYANOBILIN / D-SERINE / GLUTAMIC ACID / GLYCINE / LYSINE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Allophycocyanin alpha / Allophycocyanin beta
Similarity search - Component
Biological speciesNostoc sp. WR13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.419 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Allophycocyanin alpha
BBB: Allophycocyanin beta
CCC: Allophycocyanin alpha
DDD: Allophycocyanin beta
EEE: Allophycocyanin alpha
FFF: Allophycocyanin beta
GGG: Allophycocyanin alpha
HHH: Allophycocyanin beta
III: Allophycocyanin alpha
JJJ: Allophycocyanin beta
KKK: Allophycocyanin alpha
LLL: Allophycocyanin beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,00962
Polymers206,08812
Non-polymers11,92150
Water57,7923208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54450 Å2
ΔGint-446 kcal/mol
Surface area74460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.695, 177.726, 106.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11EEE-51-

LYS

21CCC-202-

P6G

31EEE-347-

HOH

41EEE-378-

HOH

51EEE-487-

HOH

61JJJ-552-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11Chains AAA CCC
22Chains AAA EEE
33Chains AAA GGG
44Chains AAA III
55Chains AAA KKK
66Chains BBB DDD
77Chains BBB FFF
88Chains BBB HHH
99Chains BBB JJJ
1010Chains BBB LLL
1111Chains CCC EEE
1212Chains CCC GGG
1313Chains CCC III
1414Chains CCC KKK
1515Chains DDD FFF
1616Chains DDD HHH
1717Chains DDD JJJ
1818Chains DDD LLL
1919Chains EEE GGG
2020Chains EEE III
2121Chains EEE KKK
2222Chains FFF HHH
2323Chains FFF JJJ
2424Chains FFF LLL
2525Chains GGG III
2626Chains GGG KKK
2727Chains HHH JJJ
2828Chains HHH LLL
2929Chains III KKK
3030Chains JJJ LLL

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30

-
Components

-
Allophycocyanin ... , 2 types, 12 molecules AAACCCEEEGGGIIIKKKBBBDDDFFFHHHJJJLLL

#1: Protein
Allophycocyanin alpha


Mass: 17007.270 Da / Num. of mol.: 6 / 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
Allophycocyanin beta


Mass: 17340.707 Da / Num. of mol.: 6 / 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

-
Non-polymers , 15 types, 3258 molecules

#3: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H15N2O2
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#11: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#12: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#13: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#14: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#15: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#16: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3208 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.3 % / Description: Blue color plates with orthorhombic morphology
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus screen condition H12: Precipitant mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350; Buffer system 3: 1.0M Tris (base); bicine, pH 8.5 Additives: amino acids: 0.2M Gly, DL-Ala, DL-Ser, DL-Glu, DL-Lys

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.419→106.372 Å / Num. obs: 383047 / % possible obs: 96.1 % / Redundancy: 8.7 % / Biso Wilson estimate: 19.64 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.027 / Rrim(I) all: 0.082 / Net I/σ(I): 13.8
Reflection shellResolution: 1.419→1.503 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 19080 / CC1/2: 0.623 / Rpim(I) all: 0.478 / Rrim(I) all: 1.313 / % possible all: 61.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSJune 26, 2018 (20180409)data reduction
Aimless0.7.1data scaling
autoPROC1.0.5data scaling
STARANISO1.10.15data scaling
PHASER2.8.2phasing
Coot0.8.9.2 EL (ccp4)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B33

1b33


Resolution: 1.419→106.372 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.127 / SU B: 3.366 / SU ML: 0.052 / Average fsc free: 0.9458 / Average fsc work: 0.9574 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1751 19133 4.995 %
Rwork0.1255 363914 -
all0.128 --
obs-383047 87.258 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20 Å20 Å2
2--2.665 Å20 Å2
3----3.705 Å2
Refinement stepCycle: LAST / Resolution: 1.419→106.372 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14448 0 841 3208 18497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01316564
X-RAY DIFFRACTIONr_bond_other_d0.0030.01716014
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.65922593
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5937069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.85652188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.91220.449891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.745152769
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg30.5311512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7115139
X-RAY DIFFRACTIONr_chiral_restr0.0840.22180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219177
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023430
X-RAY DIFFRACTIONr_nbd_refined0.2180.24117
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1820.214708
X-RAY DIFFRACTIONr_nbtor_refined0.1690.28000
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.25971
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.22383
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1230.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.237
X-RAY DIFFRACTIONr_nbd_other0.2140.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.2130
X-RAY DIFFRACTIONr_mcbond_it2.3922.2498078
X-RAY DIFFRACTIONr_mcbond_other2.3922.2498078
X-RAY DIFFRACTIONr_mcangle_it2.9143.38310141
X-RAY DIFFRACTIONr_mcangle_other2.9143.38410142
X-RAY DIFFRACTIONr_scbond_it3.32.6738486
X-RAY DIFFRACTIONr_scbond_other3.32.6738487
X-RAY DIFFRACTIONr_scangle_it3.9613.84112311
X-RAY DIFFRACTIONr_scangle_other3.9613.84112312
X-RAY DIFFRACTIONr_lrange_it5.39631.45721036
X-RAY DIFFRACTIONr_lrange_other4.68329.42219922
X-RAY DIFFRACTIONr_rigid_bond_restr2.503332578
X-RAY DIFFRACTIONr_ncsr_local_group_10.0920.055099
X-RAY DIFFRACTIONr_ncsr_local_group_20.0960.055068
X-RAY DIFFRACTIONr_ncsr_local_group_30.1110.055095
X-RAY DIFFRACTIONr_ncsr_local_group_40.110.055063
X-RAY DIFFRACTIONr_ncsr_local_group_50.0930.055100
X-RAY DIFFRACTIONr_ncsr_local_group_60.0940.055177
X-RAY DIFFRACTIONr_ncsr_local_group_70.0890.055234
X-RAY DIFFRACTIONr_ncsr_local_group_80.090.055159
X-RAY DIFFRACTIONr_ncsr_local_group_90.0870.055249
X-RAY DIFFRACTIONr_ncsr_local_group_100.0750.055281
X-RAY DIFFRACTIONr_ncsr_local_group_110.0950.055167
X-RAY DIFFRACTIONr_ncsr_local_group_120.0930.055233
X-RAY DIFFRACTIONr_ncsr_local_group_130.1060.055156
X-RAY DIFFRACTIONr_ncsr_local_group_140.1080.055124
X-RAY DIFFRACTIONr_ncsr_local_group_150.0970.055230
X-RAY DIFFRACTIONr_ncsr_local_group_160.0870.055268
X-RAY DIFFRACTIONr_ncsr_local_group_170.0980.055239
X-RAY DIFFRACTIONr_ncsr_local_group_180.1020.055199
X-RAY DIFFRACTIONr_ncsr_local_group_190.1030.055054
X-RAY DIFFRACTIONr_ncsr_local_group_200.0940.055158
X-RAY DIFFRACTIONr_ncsr_local_group_210.1040.055078
X-RAY DIFFRACTIONr_ncsr_local_group_220.080.055014
X-RAY DIFFRACTIONr_ncsr_local_group_230.0640.055155
X-RAY DIFFRACTIONr_ncsr_local_group_240.0840.055035
X-RAY DIFFRACTIONr_ncsr_local_group_250.1020.055115
X-RAY DIFFRACTIONr_ncsr_local_group_260.1130.055052
X-RAY DIFFRACTIONr_ncsr_local_group_270.0940.055228
X-RAY DIFFRACTIONr_ncsr_local_group_280.0960.055182
X-RAY DIFFRACTIONr_ncsr_local_group_290.1080.054995
X-RAY DIFFRACTIONr_ncsr_local_group_300.0870.055096
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
1.419-1.4560.3261570.27927750.282322400.8080.8199.09430.274
1.456-1.4960.3076490.277119570.278314180.8570.8640.12350.268
1.496-1.5390.28312100.253229660.255305760.8780.89579.06860.239
1.539-1.5860.2614320.221273020.223297450.9060.9296.60110.2
1.586-1.6380.23213870.187273280.189287420.9210.93999.90610.162
1.638-1.6960.20913800.166265420.168279230.9380.9599.99640.14
1.696-1.760.19713750.144255240.147268990.9490.9621000.117
1.76-1.8320.19513170.126246420.129259590.9550.971000.102
1.832-1.9130.17612740.115236020.118248800.9610.97499.98390.095
1.913-2.0070.1711750.114226580.117238380.9640.97699.9790.099
2.007-2.1150.15811380.107214870.11226340.9720.98199.96020.097
2.115-2.2430.15910670.099203930.102214650.9720.98199.97670.093
2.243-2.3980.14510000.086192040.089202120.9770.98699.96040.084
2.398-2.590.1569340.094179370.097188820.9730.98399.94170.095
2.59-2.8370.1538460.1164720.103173330.9730.98299.91350.107
2.837-3.1720.1627950.108149620.11157870.9720.98199.810.121
3.172-3.6620.1616840.119132430.121139620.9720.9899.74930.138
3.662-4.4840.1535940.112112170.114118690.9750.98299.51130.141
4.484-6.3350.1814580.14887500.14992910.970.97599.10670.192
6.335-106.3720.2362610.19849540.253310.9470.95297.82410.329

+
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://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