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- PDB-5fvb: CRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0 -

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Basic information

Entry
Database: PDB / ID: 5fvb
TitleCRYSTAL STRUCTURE OF PHORMIDIUM C-PHYCOERYTHRIN AT PH 5.0
Components
  • C-PHYCOERYTHRIN ALPHA SUBUNIT
  • C-PHYCOERYTHRIN BETA SUBUNIT
KeywordsPHOTOSYNTHESIS / PHORMIDIUM / C-PHYCOERYTHRIN / PEB CHROMOPHORE
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanins / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHYCOERYTHROBILIN / Phycoerythrin Alpha subunit / Phycoerythrin Beta subunit
Similarity search - Component
Biological speciesPHORMIDIUM RUBIDUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsKumar, V. / Sonani, R.R. / Sharma, M. / Gupta, G.D. / Madamwar, D.
Citation
Journal: Photosynth.Res. / Year: 2016
Title: Crystal Structure Analysis of C-Phycoerythrin from Marine Cyanobacterium Phormidium Sp. A09Dm.
Authors: Kumar, V. / Sonani, R.R. / Sharma, M. / Gupta, G.D. / Madamwar, D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Phormidium Phycoerythrin Forms Hexamers in Crystals: A Crystallographic Study.
Authors: Sonani, R.R. / Sharma, M. / Gupta, G.D. / Kumar, V. / Madamwar, D.
History
DepositionFeb 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 2.0Apr 11, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conf / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-PHYCOERYTHRIN ALPHA SUBUNIT
B: C-PHYCOERYTHRIN ALPHA SUBUNIT
C: C-PHYCOERYTHRIN ALPHA SUBUNIT
D: C-PHYCOERYTHRIN ALPHA SUBUNIT
E: C-PHYCOERYTHRIN ALPHA SUBUNIT
F: C-PHYCOERYTHRIN ALPHA SUBUNIT
G: C-PHYCOERYTHRIN ALPHA SUBUNIT
H: C-PHYCOERYTHRIN ALPHA SUBUNIT
I: C-PHYCOERYTHRIN ALPHA SUBUNIT
J: C-PHYCOERYTHRIN ALPHA SUBUNIT
K: C-PHYCOERYTHRIN ALPHA SUBUNIT
L: C-PHYCOERYTHRIN ALPHA SUBUNIT
M: C-PHYCOERYTHRIN BETA SUBUNIT
N: C-PHYCOERYTHRIN BETA SUBUNIT
O: C-PHYCOERYTHRIN BETA SUBUNIT
P: C-PHYCOERYTHRIN BETA SUBUNIT
Q: C-PHYCOERYTHRIN BETA SUBUNIT
R: C-PHYCOERYTHRIN BETA SUBUNIT
S: C-PHYCOERYTHRIN BETA SUBUNIT
T: C-PHYCOERYTHRIN BETA SUBUNIT
U: C-PHYCOERYTHRIN BETA SUBUNIT
V: C-PHYCOERYTHRIN BETA SUBUNIT
W: C-PHYCOERYTHRIN BETA SUBUNIT
X: C-PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)480,70795
Polymers444,37224
Non-polymers36,33571
Water92,2735122
1
G: C-PHYCOERYTHRIN ALPHA SUBUNIT
H: C-PHYCOERYTHRIN ALPHA SUBUNIT
I: C-PHYCOERYTHRIN ALPHA SUBUNIT
J: C-PHYCOERYTHRIN ALPHA SUBUNIT
K: C-PHYCOERYTHRIN ALPHA SUBUNIT
L: C-PHYCOERYTHRIN ALPHA SUBUNIT
S: C-PHYCOERYTHRIN BETA SUBUNIT
T: C-PHYCOERYTHRIN BETA SUBUNIT
U: C-PHYCOERYTHRIN BETA SUBUNIT
V: C-PHYCOERYTHRIN BETA SUBUNIT
W: C-PHYCOERYTHRIN BETA SUBUNIT
X: C-PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,39948
Polymers222,18612
Non-polymers18,21336
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74780 Å2
ΔGint-563.5 kcal/mol
Surface area69720 Å2
MethodPISA
2
A: C-PHYCOERYTHRIN ALPHA SUBUNIT
B: C-PHYCOERYTHRIN ALPHA SUBUNIT
C: C-PHYCOERYTHRIN ALPHA SUBUNIT
D: C-PHYCOERYTHRIN ALPHA SUBUNIT
E: C-PHYCOERYTHRIN ALPHA SUBUNIT
F: C-PHYCOERYTHRIN ALPHA SUBUNIT
M: C-PHYCOERYTHRIN BETA SUBUNIT
N: C-PHYCOERYTHRIN BETA SUBUNIT
O: C-PHYCOERYTHRIN BETA SUBUNIT
P: C-PHYCOERYTHRIN BETA SUBUNIT
Q: C-PHYCOERYTHRIN BETA SUBUNIT
R: C-PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,30747
Polymers222,18612
Non-polymers18,12135
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area74300 Å2
ΔGint-565 kcal/mol
Surface area69940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.165, 109.148, 117.680
Angle α, β, γ (deg.)78.71, 82.30, 61.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
C-PHYCOERYTHRIN ALPHA SUBUNIT


Mass: 17660.830 Da / Num. of mol.: 12 / Fragment: FRAGMENT ALPHA-CHAIN RESIDUES 1-164 / Source method: isolated from a natural source
Details: THE BACTERIUM WAS ISOLATED FROM OPEN ROCKY SHORES OF OKHA, GUJARAT, INDIA (22.3597N, 69.5375E)
Source: (natural) PHORMIDIUM RUBIDUM (bacteria) / Strain: A09DM / References: UniProt: A0A0E3W010
#2: Protein
C-PHYCOERYTHRIN BETA SUBUNIT


Mass: 19370.189 Da / Num. of mol.: 12 / Fragment: FRAGMENT BETA-CHAIN RESIDUES 1-184 / Source method: isolated from a natural source
Details: THE BACTERIUM WAS ISOLATED FROM OPEN ROCKY SHORES OF OKHA, GUJARAT, INDIA (22.3597N, 69.5375E)
Source: (natural) PHORMIDIUM RUBIDUM (bacteria) / Strain: A09DM / References: UniProt: A0A0E4G455
#3: Chemical...
ChemComp-PEB / PHYCOERYTHROBILIN / Phycoerythrobilin


Mass: 588.694 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C33H40N4O6
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsC-TERMINAL FOUR AMINO ACIDS OF THE ALPHA SUBUNIT COULD NOT BE DEDUCED FROM NUCLEOTIDE SEQUENCE ...C-TERMINAL FOUR AMINO ACIDS OF THE ALPHA SUBUNIT COULD NOT BE DEDUCED FROM NUCLEOTIDE SEQUENCE BEING PRIMER BINDING REGION, AND WERE DETERMINED FROM THE CRYSTAL STRUCTURE N-TERMINAL SEVEN AMINO ACIDS OF THE BETA SUBUNIT COULD NOT BE DEDUCED FROM NUCLEOTIDE SEQUENCE BEING PRIMER BINDING REGION, AND WERE DETERMINED FROM THE CRYSTAL STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 5
Details: 0.1M CITRATE (PH 5.0), 5% PEG-6000 AND 25% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 / Wavelength: 0.97947 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 14, 2015
RadiationMonochromator: SI (111) AND SI (220) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.93→38.89 Å / Num. obs: 338355 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 18.36 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.4
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.8 / % possible all: 92

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
autoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AQD

5aqd


Resolution: 1.93→38.891 Å / SU ML: 0.25 / σ(F): 1.96 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 17296 5.1 %
Rwork0.1832 --
obs0.186 338111 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.4 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 1.93→38.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31032 0 2646 5122 38800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734303
X-RAY DIFFRACTIONf_angle_d2.12746615
X-RAY DIFFRACTIONf_dihedral_angle_d16.05512418
X-RAY DIFFRACTIONf_chiral_restr0.0475112
X-RAY DIFFRACTIONf_plane_restr0.0056036
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9304-1.95230.32164450.25448733X-RAY DIFFRACTION78
1.9523-1.97530.34535560.252410674X-RAY DIFFRACTION96
1.9753-1.99940.31345760.226310719X-RAY DIFFRACTION96
1.9994-2.02470.28095590.219310743X-RAY DIFFRACTION96
2.0247-2.05130.28885750.219110692X-RAY DIFFRACTION97
2.0513-2.07940.29556010.219210738X-RAY DIFFRACTION97
2.0794-2.10910.29435960.209510739X-RAY DIFFRACTION96
2.1091-2.14060.26735860.204810860X-RAY DIFFRACTION97
2.1406-2.17410.26966010.203410569X-RAY DIFFRACTION97
2.1741-2.20970.27255740.206710739X-RAY DIFFRACTION97
2.2097-2.24780.26965250.199210793X-RAY DIFFRACTION97
2.2478-2.28870.26695690.20310791X-RAY DIFFRACTION97
2.2887-2.33270.28975760.211110740X-RAY DIFFRACTION97
2.3327-2.38030.28376080.207210790X-RAY DIFFRACTION97
2.3803-2.43210.2446330.190110751X-RAY DIFFRACTION97
2.4321-2.48860.26786390.198910702X-RAY DIFFRACTION97
2.4886-2.55080.27116230.198510664X-RAY DIFFRACTION97
2.5508-2.61980.25715800.190210810X-RAY DIFFRACTION97
2.6198-2.69690.2675180.189110775X-RAY DIFFRACTION97
2.6969-2.78390.2645750.188710870X-RAY DIFFRACTION97
2.7839-2.88340.23845570.182110802X-RAY DIFFRACTION97
2.8834-2.99880.25415670.185510748X-RAY DIFFRACTION97
2.9988-3.13520.2455720.184910767X-RAY DIFFRACTION97
3.1352-3.30040.21026060.174310734X-RAY DIFFRACTION97
3.3004-3.50710.21785960.17210752X-RAY DIFFRACTION97
3.5071-3.77760.21235310.165710831X-RAY DIFFRACTION97
3.7776-4.15740.20155900.158710839X-RAY DIFFRACTION98
4.1574-4.75810.18135760.14310915X-RAY DIFFRACTION98
4.7581-5.99110.18396000.151410975X-RAY DIFFRACTION99
5.9911-38.89920.16135860.150510560X-RAY DIFFRACTION95

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