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- PDB-5aqd: Crystal structure of Phormidium Phycoerythrin at pH 8.5 -

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Basic information

Entry
Database: PDB / ID: 5aqd
TitleCrystal structure of Phormidium Phycoerythrin at pH 8.5
Components(PHYCOERYTHRIN ...) x 2
KeywordsPHOTOSYNTHESIS / PHYCOBILISOME PROTEIN / PHYCOERYTHRIN ALPHA CHAIN / PHYCOERYTHRIN BETA CHAIN / PEB CHROMOPHORE / PROTEIN-CHROMOPHORE LINKAGE
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 A09DM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.121 Å
AuthorsKumar, V. / Sharma, M. / Sonani, R.R. / 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
DepositionSep 22, 2015Deposition 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_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)482,528114
Polymers444,37224
Non-polymers38,15690
Water66,8183709
1
A: PHYCOERYTHRIN ALPHA SUBUNIT
B: PHYCOERYTHRIN ALPHA SUBUNIT
C: PHYCOERYTHRIN ALPHA SUBUNIT
D: PHYCOERYTHRIN ALPHA SUBUNIT
E: PHYCOERYTHRIN ALPHA SUBUNIT
F: PHYCOERYTHRIN ALPHA SUBUNIT
M: PHYCOERYTHRIN BETA SUBUNIT
N: PHYCOERYTHRIN BETA SUBUNIT
O: PHYCOERYTHRIN BETA SUBUNIT
P: PHYCOERYTHRIN BETA SUBUNIT
Q: PHYCOERYTHRIN BETA SUBUNIT
R: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,26457
Polymers222,18612
Non-polymers19,07845
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76720 Å2
ΔGint-717.6 kcal/mol
Surface area69990 Å2
MethodPISA
2
G: PHYCOERYTHRIN ALPHA SUBUNIT
H: PHYCOERYTHRIN ALPHA SUBUNIT
I: PHYCOERYTHRIN ALPHA SUBUNIT
J: PHYCOERYTHRIN ALPHA SUBUNIT
K: PHYCOERYTHRIN ALPHA SUBUNIT
L: PHYCOERYTHRIN ALPHA SUBUNIT
S: PHYCOERYTHRIN BETA SUBUNIT
T: PHYCOERYTHRIN BETA SUBUNIT
U: PHYCOERYTHRIN BETA SUBUNIT
V: PHYCOERYTHRIN BETA SUBUNIT
W: PHYCOERYTHRIN BETA SUBUNIT
X: PHYCOERYTHRIN BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,26457
Polymers222,18612
Non-polymers19,07845
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area76910 Å2
ΔGint-716.3 kcal/mol
Surface area69590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.298, 108.360, 116.592
Angle α, β, γ (deg.)78.94, 82.50, 60.34
Int Tables number1
Space group name H-MP1

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Components

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PHYCOERYTHRIN ... , 2 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX

#1: Protein
PHYCOERYTHRIN ALPHA SUBUNIT


Mass: 17660.830 Da / Num. of mol.: 12 / Fragment: ALPHA CHAIN, RESIDUES 1-164 / Source method: isolated from a natural source
Details: PROTEIN-CHROMOPHORE LINK BETWEEN CYS-82 AND PEB-166 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-139 AND PEB-167
Source: (natural) PHORMIDIUM RUBIDUM A09DM (bacteria) / References: UniProt: A0A0E3W010
#2: Protein
PHYCOERYTHRIN BETA SUBUNIT


Mass: 19370.189 Da / Num. of mol.: 12 / Fragment: BETA CHAIN, RESIDUES 1-184 / Source method: isolated from a natural source
Details: PROTEIN-CHROMOPHORE LINK BETWEEN CYS-80 AND PEB-186 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-165 AND PEB-187 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-48 AND PEB-188 PROTEIN-CHROMOPHORE LINK BETWEEN CYS-59 AND PEB-188
Source: (natural) PHORMIDIUM RUBIDUM A09DM (bacteria) / References: UniProt: A0A0E4G455

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Non-polymers , 4 types, 3799 molecules

#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.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3709 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFOR CHAINS A TO L THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38274.3) CONSISTS OF ...FOR CHAINS A TO L THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38274.3) CONSISTS OF RESIDUES 1-160. THE FOUR C- TERMINAL AMINO ACIDS WERE DEDUCED FROM CRYSTAL STRUCTURE FOR CHAINS M TO X THE PEPTIDE SEQUENCE DEDUCED FROM GENE SEQUENCE (GENBANK CEQ38275.1) CONSISTS OF 8-184 AMINO ACIDS. SEVEN N- TERMINAL AMINO ACIDS WERE DEDUCED FROM CRYSTAL STRUCTURE

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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: 2.42 Å3/Da / Density % sol: 49.3 %
Description: STRUCTURE WAS SOLVED USING TRUNCATED MONOMER OF PDB ENTRY 2VJH. PROTEIN PHASES WERE ARRIVED AT USING 12-FOLD NCS-AVERAGING
Crystal growpH: 8.5
Details: PROTEIN CONCENTRATION 9.2 MG/ML. 1.25 M AMMONIUM SULPHATE, 0.075M TRSIS-HCL (PH 8.5), 20% 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 30, 2014
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: 2.12→29.29 Å / Num. obs: 245717 / % possible obs: 96.1 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 15.67 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.2 / % possible all: 95.1

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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 2VJH

2vjh


Resolution: 2.121→29.291 Å / SU ML: 0.26 / σ(F): 1.96 / Phase error: 24.04 / Stereochemistry target values: ML
Details: RESIDUES 21-27 OF M,N,O,P,Q,R,S,T, ,U,V,W,X CHAINS ARE DISORDERED DISORDERED REGIONS SHOW POOR ELECTRON DENISTY
RfactorNum. reflection% reflection
Rfree0.2389 12521 5.1 %
Rwork0.175 --
obs0.1782 245652 96.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.44 Å2
Refinement stepCycle: LAST / Resolution: 2.121→29.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31032 0 2742 3709 37483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834380
X-RAY DIFFRACTIONf_angle_d2.13846728
X-RAY DIFFRACTIONf_dihedral_angle_d16.21112420
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 (%)
2.1209-2.1450.30373480.22117497X-RAY DIFFRACTION93
2.145-2.17020.2884080.20777849X-RAY DIFFRACTION96
2.1702-2.19670.28264140.19877698X-RAY DIFFRACTION96
2.1967-2.22450.27514310.19457731X-RAY DIFFRACTION96
2.2245-2.25370.27733800.19887684X-RAY DIFFRACTION94
2.2537-2.28460.27844400.19217693X-RAY DIFFRACTION95
2.2846-2.31720.26114490.1837768X-RAY DIFFRACTION96
2.3172-2.35180.27954210.19427791X-RAY DIFFRACTION96
2.3518-2.38850.2933980.19147709X-RAY DIFFRACTION96
2.3885-2.42770.26184370.18257815X-RAY DIFFRACTION96
2.4277-2.46950.283870.18357827X-RAY DIFFRACTION96
2.4695-2.51440.25374190.18167821X-RAY DIFFRACTION96
2.5144-2.56270.26643980.17767831X-RAY DIFFRACTION96
2.5627-2.6150.25553820.18297840X-RAY DIFFRACTION97
2.615-2.67180.29344100.19047761X-RAY DIFFRACTION96
2.6718-2.73390.26754350.1847811X-RAY DIFFRACTION97
2.7339-2.80230.2454020.1727876X-RAY DIFFRACTION96
2.8023-2.8780.25514540.18087773X-RAY DIFFRACTION97
2.878-2.96260.25655060.18297753X-RAY DIFFRACTION97
2.9626-3.05810.24174740.17117771X-RAY DIFFRACTION97
3.0581-3.16730.25054340.1737829X-RAY DIFFRACTION97
3.1673-3.29390.22794070.17077856X-RAY DIFFRACTION97
3.2939-3.44360.21683350.16947861X-RAY DIFFRACTION96
3.4436-3.62490.21653650.16047901X-RAY DIFFRACTION96
3.6249-3.85150.20173650.15197753X-RAY DIFFRACTION96
3.8515-4.14810.19884150.14927727X-RAY DIFFRACTION95
4.1481-4.56420.18484220.14597770X-RAY DIFFRACTION96
4.5642-5.22140.21464620.16047750X-RAY DIFFRACTION97
5.2214-6.56610.21014970.1827801X-RAY DIFFRACTION97
6.5661-29.29350.18954260.17727584X-RAY DIFFRACTION94

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