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- PDB-7f86: Crystal structure of Phycoerythrin from Halomicronema Sp. R31DM -

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Basic information

Entry
Database: PDB / ID: 7f86
TitleCrystal structure of Phycoerythrin from Halomicronema Sp. R31DM
Components
  • Phycoerythrin alpha subunit
  • Phycoerythrin beta subunit
KeywordsPHOTOSYNTHESIS / Light harvesting / Phycobiliproteins / Cyanobacteria
Function / homologyPHYCOERYTHROBILIN
Function and homology information
Biological speciesHalomicronema sp. R31DM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsPatel, S.N. / Gupta, G.D. / Sonani, R.R. / Singh, N.K. / Kumar, V. / Madamwar, D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR15686/AAQ/3/811/2016 India
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2023
Title: Crystal structure analysis of phycoerythrin from marine cyanobacterium Halomicronema .
Authors: Patel, S.N. / Sonani, R.R. / Gupta, G.D. / Singh, N.K. / Kumar, V. / Madamwar, D.
History
DepositionJul 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
M: Phycoerythrin beta subunit
A: Phycoerythrin alpha subunit
D: Phycoerythrin alpha subunit
B: Phycoerythrin alpha subunit
F: Phycoerythrin alpha subunit
H: Phycoerythrin alpha subunit
J: Phycoerythrin alpha subunit
L: Phycoerythrin alpha subunit
O: Phycoerythrin alpha subunit
Q: Phycoerythrin alpha subunit
U: Phycoerythrin alpha subunit
W: Phycoerythrin alpha subunit
C: Phycoerythrin beta subunit
E: Phycoerythrin beta subunit
G: Phycoerythrin beta subunit
I: Phycoerythrin beta subunit
K: Phycoerythrin beta subunit
N: Phycoerythrin beta subunit
P: Phycoerythrin beta subunit
R: Phycoerythrin beta subunit
T: Phycoerythrin beta subunit
V: Phycoerythrin beta subunit
X: Phycoerythrin beta subunit
Y: Phycoerythrin alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,85984
Polymers445,53824
Non-polymers35,32260
Water50,0102776
1
M: Phycoerythrin beta subunit
A: Phycoerythrin alpha subunit
D: Phycoerythrin alpha subunit
H: Phycoerythrin alpha subunit
W: Phycoerythrin alpha subunit
E: Phycoerythrin beta subunit
I: Phycoerythrin beta subunit
X: Phycoerythrin beta subunit
hetero molecules

Q: Phycoerythrin alpha subunit
R: Phycoerythrin beta subunit
T: Phycoerythrin beta subunit
Y: Phycoerythrin alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,43042
Polymers222,76912
Non-polymers17,66130
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area73890 Å2
ΔGint-547 kcal/mol
Surface area71380 Å2
MethodPISA
2
B: Phycoerythrin alpha subunit
F: Phycoerythrin alpha subunit
J: Phycoerythrin alpha subunit
L: Phycoerythrin alpha subunit
O: Phycoerythrin alpha subunit
U: Phycoerythrin alpha subunit
C: Phycoerythrin beta subunit
G: Phycoerythrin beta subunit
K: Phycoerythrin beta subunit
N: Phycoerythrin beta subunit
P: Phycoerythrin beta subunit
V: Phycoerythrin beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,43042
Polymers222,76912
Non-polymers17,66130
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74260 Å2
ΔGint-546 kcal/mol
Surface area71030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.590, 108.630, 116.930
Angle α, β, γ (deg.)78.370, 82.530, 62.110
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Phycoerythrin beta subunit


Mass: 19367.168 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Halomicronema sp. R31DM (bacteria)
#2: Protein
Phycoerythrin alpha subunit


Mass: 17760.973 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Halomicronema sp. R31DM (bacteria)
#3: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN


Mass: 588.694 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2776 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.21→42.17 Å / Num. obs: 225119 / % possible obs: 97.3 % / Redundancy: 3.9 % / CC1/2: 0.997 / Net I/σ(I): 15.6
Reflection shellResolution: 2.21→2.21 Å / Num. unique obs: 11005 / CC1/2: 0.974

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NB4

5nb4


Resolution: 2.21→42.17 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.803 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2101 11103 4.9 %RANDOM
Rwork0.1631 ---
obs0.1654 214013 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.67 Å2 / Biso mean: 17.951 Å2 / Biso min: 1.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.12 Å2-0.16 Å2
2---0.65 Å2-0.16 Å2
3---1.04 Å2
Refinement stepCycle: final / Resolution: 2.21→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31086 0 2580 2776 36442
Biso mean--20.82 26.52 -
Num. residues----4176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01334292
X-RAY DIFFRACTIONr_bond_other_d0.0010.01731889
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.65646678
X-RAY DIFFRACTIONr_angle_other_deg1.3751.58373285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96154156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96619.3421959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.388155183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.78815273
X-RAY DIFFRACTIONr_chiral_restr0.0830.24430
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0240522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027033
LS refinement shellResolution: 2.21→2.267 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 835 -
Rwork0.157 15593 -
all-16428 -
obs--96.29 %

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